Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c199' (ED25519) to the list of known hosts.
Running: /usr/bin/copr-rpmbuild --verbose --drop-resultdir --build-id 5017372 --chroot fedora-rawhide-x86_64 --detached
Version: 0.61
PID: 5601
Logging PID: 5602
Task:
{'appstream': False,
 'background': True,
 'build_id': 5017372,
 'buildroot_pkgs': [],
 'chroot': 'fedora-rawhide-x86_64',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': '12c13c6b3f30897de8a06524ea30d40006885494',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/djdelorie/make-4.4/percolator',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'percolator',
 'package_version': '3.05-10',
 'project_dirname': 'make-4.4',
 'project_name': 'make-4.4',
 'project_owner': 'djdelorie',
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/djdelorie/make-4.4/fedora-rawhide-x86_64/',
            'id': 'copr_base',
            'name': 'Copr repository'}],
 'sandbox': 'djdelorie/make-4.4--djdelorie',
 'source_json': {},
 'source_type': None,
 'submitter': 'djdelorie',
 'tags': [],
 'task_id': '5017372-fedora-rawhide-x86_64',
 'timeout': 108000,
 'uses_devel_repo': False,
 'with_opts': [],
 'without_opts': []}

Running: git clone https://copr-dist-git.fedorainfracloud.org/git/djdelorie/make-4.4/percolator /var/lib/copr-rpmbuild/workspace/workdir-_t6tuudt/percolator --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/djdelorie/make-4.4/percolator', '/var/lib/copr-rpmbuild/workspace/workdir-_t6tuudt/percolator', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-_t6tuudt/percolator'...

Running: git checkout 12c13c6b3f30897de8a06524ea30d40006885494

cmd: ['git', 'checkout', '12c13c6b3f30897de8a06524ea30d40006885494']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-_t6tuudt/percolator
rc: 0
stdout: 
stderr: Note: switching to '12c13c6b3f30897de8a06524ea30d40006885494'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 12c13c6 automatic import of percolator

Running: copr-distgit-client sources

/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated
cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-_t6tuudt/percolator
rc: 0
stdout: 
stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD
INFO: Reading stdout from command: git rev-parse HEAD
INFO: Reading sources specification file: sources
INFO: Downloading percolator-rel-3-05.tar.gz
INFO: Calling: curl -H Pragma: -o percolator-rel-3-05.tar.gz --location --remote-time --show-error --fail https://copr-dist-git.fedorainfracloud.org/repo/pkgs/djdelorie/make-4.4/percolator/percolator-rel-3-05.tar.gz/md5/46a10770d808f8db4bd5bd2d30c9be4d/percolator-rel-3-05.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 11.5M  100 11.5M    0     0  18.5M      0 --:--:-- --:--:-- --:--:-- 18.5M
INFO: Reading stdout from command: md5sum percolator-rel-3-05.tar.gz
INFO: Downloading yeast-01.sqt.tar.gz
INFO: Calling: curl -H Pragma: -o yeast-01.sqt.tar.gz --location --remote-time --show-error --fail https://copr-dist-git.fedorainfracloud.org/repo/pkgs/djdelorie/make-4.4/percolator/yeast-01.sqt.tar.gz/md5/81e1997e1c1c193cbfcd4eb54c706af9/yeast-01.sqt.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 47.9M  100 47.9M    0     0  10.0M      0  0:00:04  0:00:04 --:--:-- 10.2M
INFO: Reading stdout from command: md5sum yeast-01.sqt.tar.gz

Running (timeout=108000): unbuffer mock --buildsrpm --spec /var/lib/copr-rpmbuild/workspace/workdir-_t6tuudt/percolator/percolator.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-_t6tuudt/percolator --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1668321698.617486 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 3.3 starting (python version = 3.10.4, NVR = mock-3.3-1.fc35)...
Start(bootstrap): init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish(bootstrap): init plugins
Start: init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish: init plugins
INFO: Signal handler active
Start: run
INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-_t6tuudt/percolator/percolator.spec)  Config(fedora-rawhide-x86_64)
Start: clean chroot
Finish: clean chroot
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1668321698.617486/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
INFO: enabled HW Info plugin
Mock Version: 3.3
INFO: Mock Version: 3.3
Start(bootstrap): dnf install
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Updating Subscription Management repositories.
Unable to read consumer identity

This system is not registered with an entitlement server. You can use subscription-manager to register.

Copr repository                                  43 MB/s |  34 MB     00:00    
fedora                                          8.3 MB/s |  65 MB     00:07    
Last metadata expiration check: 0:00:07 ago on Sun Nov 13 06:41:50 2022.
Dependencies resolved.
================================================================================
 Package                      Arch   Version                    Repo       Size
================================================================================
Installing:
 dnf                          noarch 4.14.0-1.fc38              fedora    480 k
 dnf-plugins-core             noarch 4.3.1-1.fc38               fedora     34 k
Installing dependencies:
 alternatives                 x86_64 1.21-1.fc38                copr_base  38 k
 audit-libs                   x86_64 3.0.9-1.fc38               copr_base 116 k
 basesystem                   noarch 11-14.fc37                 fedora    7.0 k
 bash                         x86_64 5.2.2-2.fc38               copr_base 1.8 M
 bzip2-libs                   x86_64 1.0.8-12.fc38              copr_base  42 k
 ca-certificates              noarch 2022.2.54-5.fc37           fedora    829 k
 coreutils                    x86_64 9.1-8.fc38                 copr_base 1.1 M
 coreutils-common             x86_64 9.1-8.fc38                 copr_base 2.0 M
 crypto-policies              noarch 20221110-1.git87a75f4.fc38 fedora     90 k
 curl                         x86_64 7.86.0-2.fc38              fedora    334 k
 cyrus-sasl-lib               x86_64 2.1.28-8.fc38              copr_base 794 k
 dbus-libs                    x86_64 1:1.14.4-1.fc38            copr_base 156 k
 dnf-data                     noarch 4.14.0-1.fc38              fedora     43 k
 elfutils-default-yama-scope  noarch 0.188-3.fc38               fedora     15 k
 elfutils-libelf              x86_64 0.188-3.fc38               fedora    196 k
 elfutils-libs                x86_64 0.188-3.fc38               fedora    257 k
 expat                        x86_64 2.4.8-2.fc38               copr_base 110 k
 fedora-gpg-keys              noarch 38-0.3                     fedora    125 k
 fedora-release               noarch 38-0.4                     fedora     11 k
 fedora-release-common        noarch 38-0.4                     fedora     22 k
 fedora-release-identity-basic
                              noarch 38-0.4                     fedora     12 k
 fedora-repos                 noarch 38-0.3                     fedora     10 k
 fedora-repos-rawhide         noarch 38-0.3                     fedora    9.7 k
 file-libs                    x86_64 5.42-4.fc38                copr_base 676 k
 filesystem                   x86_64 3.18-2.fc37                fedora    1.1 M
 findutils                    x86_64 1:4.9.0-2.fc38             copr_base 483 k
 gawk                         x86_64 5.1.1-4.fc38               copr_base 1.0 M
 gdbm-libs                    x86_64 1:1.23-2.fc38              copr_base  56 k
 glib2                        x86_64 2.74.1-2.fc38              fedora    2.7 M
 glibc                        x86_64 2.36.9000-13.fc38          fedora    2.1 M
 glibc-common                 x86_64 2.36.9000-13.fc38          fedora    304 k
 glibc-minimal-langpack       x86_64 2.36.9000-13.fc38          fedora     25 k
 gmp                          x86_64 1:6.2.1-3.fc38             copr_base 316 k
 gnupg2                       x86_64 2.3.8-1.fc38               copr_base 2.5 M
 gnutls                       x86_64 3.7.8-9.fc38               fedora    1.1 M
 gpgme                        x86_64 1.17.0-4.fc38              copr_base 211 k
 grep                         x86_64 3.8-1.fc38                 copr_base 282 k
 ima-evm-utils                x86_64 1.4-6.fc38                 copr_base  63 k
 json-c                       x86_64 0.16-3.fc38                fedora     41 k
 keyutils-libs                x86_64 1.6.1-5.fc38               copr_base  32 k
 krb5-libs                    x86_64 1.19.2-11.fc38.1           copr_base 724 k
 libacl                       x86_64 2.3.1-4.fc38               copr_base  24 k
 libarchive                   x86_64 3.6.1-2.fc38               copr_base 397 k
 libassuan                    x86_64 2.5.5-5.fc38               copr_base  67 k
 libattr                      x86_64 2.5.1-5.fc38               copr_base  18 k
 libb2                        x86_64 0.98.1-7.fc38              copr_base  25 k
 libblkid                     x86_64 2.38.1-2.fc38              copr_base 107 k
 libbrotli                    x86_64 1.0.9-9.fc37               fedora    315 k
 libcap                       x86_64 2.48-5.fc38                copr_base  67 k
 libcap-ng                    x86_64 0.8.3-3.fc38               copr_base  33 k
 libcom_err                   x86_64 1.46.5-3.fc38              copr_base  26 k
 libcomps                     x86_64 0.1.18-4.fc38              copr_base  77 k
 libcurl                      x86_64 7.86.0-2.fc38              fedora    305 k
 libdnf                       x86_64 0.68.0-1.fc38              fedora    673 k
 libevent                     x86_64 2.1.12-7.fc38              copr_base 259 k
 libffi                       x86_64 3.4.4-1.fc38               fedora     38 k
 libfsverity                  x86_64 1.4-8.fc38                 copr_base  20 k
 libgcc                       x86_64 12.2.1-3.fc38              fedora    108 k
 libgcrypt                    x86_64 1.10.1-5.fc38              fedora    513 k
 libgomp                      x86_64 12.2.1-3.fc38              fedora    295 k
 libgpg-error                 x86_64 1.46-1.fc38                copr_base 222 k
 libidn2                      x86_64 2.3.4-1.fc38               copr_base 154 k
 libksba                      x86_64 1.6.2-1.fc38               copr_base 158 k
 libmodulemd                  x86_64 2.14.0-4.fc37              fedora    234 k
 libmount                     x86_64 2.38.1-2.fc38              copr_base 136 k
 libnghttp2                   x86_64 1.50.0-1.fc38              copr_base  75 k
 libnsl2                      x86_64 2.0.0-4.fc38               copr_base  31 k
 libpsl                       x86_64 0.21.1-6.fc38              copr_base  64 k
 librepo                      x86_64 1.14.4-1.fc38              fedora     94 k
 libreport-filesystem         noarch 2.17.6-1.fc38              fedora     14 k
 libselinux                   x86_64 3.4-5.fc38                 copr_base  86 k
 libsemanage                  x86_64 3.4-5.fc38                 copr_base 120 k
 libsepol                     x86_64 3.4-3.fc38                 copr_base 322 k
 libsigsegv                   x86_64 2.14-3.fc38                copr_base  27 k
 libsmartcols                 x86_64 2.38.1-2.fc38              copr_base  65 k
 libsolv                      x86_64 0.7.22-3.fc37              fedora    405 k
 libssh                       x86_64 0.10.4-2.fc38              fedora    209 k
 libssh-config                noarch 0.10.4-2.fc38              fedora    8.8 k
 libstdc++                    x86_64 12.2.1-3.fc38              fedora    799 k
 libtasn1                     x86_64 4.18.0-3.fc38              copr_base  75 k
 libtirpc                     x86_64 1.3.3-0.fc38               copr_base  94 k
 libunistring                 x86_64 1.0-2.fc38                 copr_base 549 k
 libuuid                      x86_64 2.38.1-2.fc38              copr_base  28 k
 libverto                     x86_64 0.3.2-4.fc38               copr_base  21 k
 libxcrypt                    x86_64 4.4.30-3.fc38              fedora    118 k
 libxml2                      x86_64 2.10.3-2.fc38              fedora    705 k
 libyaml                      x86_64 0.2.5-8.fc38               copr_base  60 k
 libzstd                      x86_64 1.5.2-3.fc38               copr_base 295 k
 lua-libs                     x86_64 5.4.4-6.fc38               copr_base 132 k
 lz4-libs                     x86_64 1.9.3-5.fc38               copr_base  71 k
 mpdecimal                    x86_64 2.5.1-4.fc38               copr_base 102 k
 mpfr                         x86_64 4.1.0-10.fc38              copr_base 331 k
 ncurses-base                 noarch 6.3-3.20220501.fc38        copr_base  62 k
 ncurses-libs                 x86_64 6.3-3.20220501.fc38        copr_base 329 k
 nettle                       x86_64 3.8-2.fc38                 copr_base 414 k
 npth                         x86_64 1.6-10.fc38                copr_base  25 k
 openldap                     x86_64 2.6.3-1.fc38               fedora    254 k
 openssl-libs                 x86_64 1:3.0.5-6.fc38             fedora    2.1 M
 p11-kit                      x86_64 0.24.1-3.fc37              fedora    376 k
 p11-kit-trust                x86_64 0.24.1-3.fc37              fedora    138 k
 pcre2                        x86_64 10.40-1.fc38.1             copr_base 237 k
 pcre2-syntax                 noarch 10.40-1.fc38.1             copr_base 143 k
 popt                         x86_64 1.19-1.fc38                copr_base  59 k
 publicsuffix-list-dafsa      noarch 20210518-5.fc37            fedora     58 k
 python-pip-wheel             noarch 22.2.2-2.fc38              fedora    1.4 M
 python-setuptools-wheel      noarch 65.5.1-1.fc38              fedora    715 k
 python3                      x86_64 3.11.0-1.fc38              fedora     27 k
 python3-dateutil             noarch 1:2.8.2-4.fc38             copr_base 350 k
 python3-dbus                 x86_64 1.3.2-1.fc38               copr_base 147 k
 python3-distro               noarch 1.8.0-1.fc38               fedora     49 k
 python3-dnf                  noarch 4.14.0-1.fc38              fedora    607 k
 python3-dnf-plugins-core     noarch 4.3.1-1.fc38               fedora    277 k
 python3-gpg                  x86_64 1.17.0-4.fc38              copr_base 280 k
 python3-hawkey               x86_64 0.68.0-1.fc38              fedora    108 k
 python3-libcomps             x86_64 0.1.18-4.fc38              copr_base  48 k
 python3-libdnf               x86_64 0.68.0-1.fc38              fedora    818 k
 python3-libs                 x86_64 3.11.0-1.fc38              fedora    9.6 M
 python3-rpm                  x86_64 4.18.0-6.fc38              fedora     94 k
 python3-six                  noarch 1.16.0-8.fc37              fedora     42 k
 readline                     x86_64 8.2-2.fc38                 copr_base 211 k
 rpm                          x86_64 4.18.0-6.fc38              fedora    572 k
 rpm-build-libs               x86_64 4.18.0-6.fc38              fedora     94 k
 rpm-libs                     x86_64 4.18.0-6.fc38              fedora    320 k
 rpm-sign-libs                x86_64 4.18.0-6.fc38              fedora     27 k
 sed                          x86_64 4.8-11.fc38                copr_base 297 k
 setup                        noarch 2.14.2-1.fc38              copr_base 145 k
 shadow-utils                 x86_64 2:4.13-1.fc38              fedora    1.3 M
 sqlite-libs                  x86_64 3.39.4-1.fc38              copr_base 659 k
 systemd-libs                 x86_64 252.1-588.fc38             fedora    631 k
 tpm2-tss                     x86_64 3.2.0-3.fc38               copr_base 596 k
 tzdata                       noarch 2022f-1.fc38               copr_base 431 k
 xz-libs                      x86_64 5.2.7-1.fc38               copr_base  93 k
 zchunk-libs                  x86_64 1.2.3-1.fc38               fedora     51 k
 zlib                         x86_64 1.2.12-5.fc38              copr_base  94 k

Transaction Summary
================================================================================
Install  136 Packages

Total download size: 55 M
Installed size: 196 M
Downloading Packages:
(1/136): alternatives-1.21-1.fc38.x86_64.rpm    860 kB/s |  38 kB     00:00    
(2/136): bzip2-libs-1.0.8-12.fc38.x86_64.rpm    4.0 MB/s |  42 kB     00:00    
(3/136): audit-libs-3.0.9-1.fc38.x86_64.rpm     1.9 MB/s | 116 kB     00:00    
(4/136): bash-5.2.2-2.fc38.x86_64.rpm            22 MB/s | 1.8 MB     00:00    
(5/136): coreutils-9.1-8.fc38.x86_64.rpm         24 MB/s | 1.1 MB     00:00    
(6/136): coreutils-common-9.1-8.fc38.x86_64.rpm  34 MB/s | 2.0 MB     00:00    
(7/136): cyrus-sasl-lib-2.1.28-8.fc38.x86_64.rp  18 MB/s | 794 kB     00:00    
(8/136): dbus-libs-1.14.4-1.fc38.x86_64.rpm     4.0 MB/s | 156 kB     00:00    
(9/136): expat-2.4.8-2.fc38.x86_64.rpm          6.0 MB/s | 110 kB     00:00    
(10/136): file-libs-5.42-4.fc38.x86_64.rpm       29 MB/s | 676 kB     00:00    
(11/136): findutils-4.9.0-2.fc38.x86_64.rpm      34 MB/s | 483 kB     00:00    
(12/136): gawk-5.1.1-4.fc38.x86_64.rpm           42 MB/s | 1.0 MB     00:00    
(13/136): gdbm-libs-1.23-2.fc38.x86_64.rpm      3.9 MB/s |  56 kB     00:00    
(14/136): gmp-6.2.1-3.fc38.x86_64.rpm            26 MB/s | 316 kB     00:00    
(15/136): gnupg2-2.3.8-1.fc38.x86_64.rpm         65 MB/s | 2.5 MB     00:00    
(16/136): gpgme-1.17.0-4.fc38.x86_64.rpm        5.1 MB/s | 211 kB     00:00    
(17/136): grep-3.8-1.fc38.x86_64.rpm            7.1 MB/s | 282 kB     00:00    
(18/136): ima-evm-utils-1.4-6.fc38.x86_64.rpm   6.8 MB/s |  63 kB     00:00    
(19/136): keyutils-libs-1.6.1-5.fc38.x86_64.rpm 3.4 MB/s |  32 kB     00:00    
(20/136): krb5-libs-1.19.2-11.fc38.1.x86_64.rpm  45 MB/s | 724 kB     00:00    
(21/136): libacl-2.3.1-4.fc38.x86_64.rpm        2.7 MB/s |  24 kB     00:00    
(22/136): libarchive-3.6.1-2.fc38.x86_64.rpm     32 MB/s | 397 kB     00:00    
(23/136): libassuan-2.5.5-5.fc38.x86_64.rpm     7.5 MB/s |  67 kB     00:00    
(24/136): libattr-2.5.1-5.fc38.x86_64.rpm       2.2 MB/s |  18 kB     00:00    
(25/136): libb2-0.98.1-7.fc38.x86_64.rpm        3.0 MB/s |  25 kB     00:00    
(26/136): libblkid-2.38.1-2.fc38.x86_64.rpm      12 MB/s | 107 kB     00:00    
(27/136): libcap-2.48-5.fc38.x86_64.rpm         7.1 MB/s |  67 kB     00:00    
(28/136): libcap-ng-0.8.3-3.fc38.x86_64.rpm     3.9 MB/s |  33 kB     00:00    
(29/136): libcom_err-1.46.5-3.fc38.x86_64.rpm   3.0 MB/s |  26 kB     00:00    
(30/136): libcomps-0.1.18-4.fc38.x86_64.rpm     7.9 MB/s |  77 kB     00:00    
(31/136): libevent-2.1.12-7.fc38.x86_64.rpm      23 MB/s | 259 kB     00:00    
(32/136): libfsverity-1.4-8.fc38.x86_64.rpm     2.3 MB/s |  20 kB     00:00    
(33/136): libgpg-error-1.46-1.fc38.x86_64.rpm    21 MB/s | 222 kB     00:00    
(34/136): libidn2-2.3.4-1.fc38.x86_64.rpm        16 MB/s | 154 kB     00:00    
(35/136): libksba-1.6.2-1.fc38.x86_64.rpm        16 MB/s | 158 kB     00:00    
(36/136): libmount-2.38.1-2.fc38.x86_64.rpm      14 MB/s | 136 kB     00:00    
(37/136): libnghttp2-1.50.0-1.fc38.x86_64.rpm   8.4 MB/s |  75 kB     00:00    
(38/136): libnsl2-2.0.0-4.fc38.x86_64.rpm       3.6 MB/s |  31 kB     00:00    
(39/136): libpsl-0.21.1-6.fc38.x86_64.rpm       4.9 MB/s |  64 kB     00:00    
(40/136): libselinux-3.4-5.fc38.x86_64.rpm      6.0 MB/s |  86 kB     00:00    
(41/136): libsemanage-3.4-5.fc38.x86_64.rpm     7.7 MB/s | 120 kB     00:00    
(42/136): libsepol-3.4-3.fc38.x86_64.rpm         23 MB/s | 322 kB     00:00    
(43/136): libsigsegv-2.14-3.fc38.x86_64.rpm     2.5 MB/s |  27 kB     00:00    
(44/136): libsmartcols-2.38.1-2.fc38.x86_64.rpm 7.2 MB/s |  65 kB     00:00    
(45/136): libtasn1-4.18.0-3.fc38.x86_64.rpm     8.4 MB/s |  75 kB     00:00    
(46/136): libtirpc-1.3.3-0.fc38.x86_64.rpm      9.6 MB/s |  94 kB     00:00    
(47/136): libunistring-1.0-2.fc38.x86_64.rpm     32 MB/s | 549 kB     00:00    
(48/136): libuuid-2.38.1-2.fc38.x86_64.rpm      1.9 MB/s |  28 kB     00:00    
(49/136): libverto-0.3.2-4.fc38.x86_64.rpm      1.4 MB/s |  21 kB     00:00    
(50/136): libyaml-0.2.5-8.fc38.x86_64.rpm       3.7 MB/s |  60 kB     00:00    
(51/136): libzstd-1.5.2-3.fc38.x86_64.rpm        15 MB/s | 295 kB     00:00    
(52/136): lua-libs-5.4.4-6.fc38.x86_64.rpm      6.7 MB/s | 132 kB     00:00    
(53/136): lz4-libs-1.9.3-5.fc38.x86_64.rpm      6.0 MB/s |  71 kB     00:00    
(54/136): mpdecimal-2.5.1-4.fc38.x86_64.rpm      10 MB/s | 102 kB     00:00    
(55/136): mpfr-4.1.0-10.fc38.x86_64.rpm          25 MB/s | 331 kB     00:00    
(56/136): ncurses-base-6.3-3.20220501.fc38.noar 4.7 MB/s |  62 kB     00:00    
(57/136): ncurses-libs-6.3-3.20220501.fc38.x86_  24 MB/s | 329 kB     00:00    
(58/136): nettle-3.8-2.fc38.x86_64.rpm           31 MB/s | 414 kB     00:00    
(59/136): npth-1.6-10.fc38.x86_64.rpm           1.8 MB/s |  25 kB     00:00    
(60/136): pcre2-10.40-1.fc38.1.x86_64.rpm        13 MB/s | 237 kB     00:00    
(61/136): pcre2-syntax-10.40-1.fc38.1.noarch.rp 7.9 MB/s | 143 kB     00:00    
(62/136): popt-1.19-1.fc38.x86_64.rpm           3.2 MB/s |  59 kB     00:00    
(63/136): python3-dateutil-2.8.2-4.fc38.noarch. 8.2 MB/s | 350 kB     00:00    
(64/136): python3-dbus-1.3.2-1.fc38.x86_64.rpm  4.0 MB/s | 147 kB     00:00    
(65/136): python3-gpg-1.17.0-4.fc38.x86_64.rpm  6.8 MB/s | 280 kB     00:00    
(66/136): python3-libcomps-0.1.18-4.fc38.x86_64 4.0 MB/s |  48 kB     00:00    
(67/136): readline-8.2-2.fc38.x86_64.rpm         14 MB/s | 211 kB     00:00    
(68/136): sed-4.8-11.fc38.x86_64.rpm             18 MB/s | 297 kB     00:00    
(69/136): setup-2.14.2-1.fc38.noarch.rpm         11 MB/s | 145 kB     00:00    
(70/136): sqlite-libs-3.39.4-1.fc38.x86_64.rpm   31 MB/s | 659 kB     00:00    
(71/136): tpm2-tss-3.2.0-3.fc38.x86_64.rpm       11 MB/s | 596 kB     00:00    
(72/136): tzdata-2022f-1.fc38.noarch.rpm        8.2 MB/s | 431 kB     00:00    
(73/136): xz-libs-5.2.7-1.fc38.x86_64.rpm       2.3 MB/s |  93 kB     00:00    
(74/136): zlib-1.2.12-5.fc38.x86_64.rpm         9.9 MB/s |  94 kB     00:00    
(75/136): basesystem-11-14.fc37.noarch.rpm      119 kB/s | 7.0 kB     00:00    
(76/136): crypto-policies-20221110-1.git87a75f4 693 kB/s |  90 kB     00:00    
(77/136): curl-7.86.0-2.fc38.x86_64.rpm         2.6 MB/s | 334 kB     00:00    
(78/136): ca-certificates-2022.2.54-5.fc37.noar 3.7 MB/s | 829 kB     00:00    
(79/136): dnf-data-4.14.0-1.fc38.noarch.rpm     1.1 MB/s |  43 kB     00:00    
(80/136): dnf-4.14.0-1.fc38.noarch.rpm          5.7 MB/s | 480 kB     00:00    
(81/136): dnf-plugins-core-4.3.1-1.fc38.noarch. 1.7 MB/s |  34 kB     00:00    
(82/136): elfutils-default-yama-scope-0.188-3.f 808 kB/s |  15 kB     00:00    
(83/136): elfutils-libelf-0.188-3.fc38.x86_64.r 7.3 MB/s | 196 kB     00:00    
(84/136): elfutils-libs-0.188-3.fc38.x86_64.rpm  10 MB/s | 257 kB     00:00    
(85/136): fedora-gpg-keys-38-0.3.noarch.rpm     5.2 MB/s | 125 kB     00:00    
(86/136): fedora-release-38-0.4.noarch.rpm      580 kB/s |  11 kB     00:00    
(87/136): fedora-release-common-38-0.4.noarch.r 1.1 MB/s |  22 kB     00:00    
(88/136): fedora-release-identity-basic-38-0.4. 629 kB/s |  12 kB     00:00    
(89/136): fedora-repos-38-0.3.noarch.rpm        539 kB/s |  10 kB     00:00    
(90/136): fedora-repos-rawhide-38-0.3.noarch.rp 513 kB/s | 9.7 kB     00:00    
(91/136): filesystem-3.18-2.fc37.x86_64.rpm      17 MB/s | 1.1 MB     00:00    
(92/136): glibc-2.36.9000-13.fc38.x86_64.rpm     30 MB/s | 2.1 MB     00:00    
(93/136): glib2-2.74.1-2.fc38.x86_64.rpm         31 MB/s | 2.7 MB     00:00    
(94/136): glibc-common-2.36.9000-13.fc38.x86_64 7.4 MB/s | 304 kB     00:00    
(95/136): glibc-minimal-langpack-2.36.9000-13.f 1.3 MB/s |  25 kB     00:00    
(96/136): gnutls-3.7.8-9.fc38.x86_64.rpm         32 MB/s | 1.1 MB     00:00    
(97/136): json-c-0.16-3.fc38.x86_64.rpm         1.7 MB/s |  41 kB     00:00    
(98/136): libbrotli-1.0.9-9.fc37.x86_64.rpm      12 MB/s | 315 kB     00:00    
(99/136): libcurl-7.86.0-2.fc38.x86_64.rpm       11 MB/s | 305 kB     00:00    
(100/136): libdnf-0.68.0-1.fc38.x86_64.rpm       23 MB/s | 673 kB     00:00    
(101/136): libffi-3.4.4-1.fc38.x86_64.rpm       1.6 MB/s |  38 kB     00:00    
(102/136): libgcc-12.2.1-3.fc38.x86_64.rpm      5.2 MB/s | 108 kB     00:00    
(103/136): libgomp-12.2.1-3.fc38.x86_64.rpm      10 MB/s | 295 kB     00:00    
(104/136): libgcrypt-1.10.1-5.fc38.x86_64.rpm    12 MB/s | 513 kB     00:00    
(105/136): libmodulemd-2.14.0-4.fc37.x86_64.rpm 5.1 MB/s | 234 kB     00:00    
(106/136): librepo-1.14.4-1.fc38.x86_64.rpm     2.3 MB/s |  94 kB     00:00    
(107/136): libreport-filesystem-2.17.6-1.fc38.n 510 kB/s |  14 kB     00:00    
(108/136): libsolv-0.7.22-3.fc37.x86_64.rpm      16 MB/s | 405 kB     00:00    
(109/136): libssh-config-0.10.4-2.fc38.noarch.r 440 kB/s | 8.8 kB     00:00    
(110/136): libssh-0.10.4-2.fc38.x86_64.rpm      9.4 MB/s | 209 kB     00:00    
(111/136): libxcrypt-4.4.30-3.fc38.x86_64.rpm   5.4 MB/s | 118 kB     00:00    
(112/136): libstdc++-12.2.1-3.fc38.x86_64.rpm    24 MB/s | 799 kB     00:00    
(113/136): libxml2-2.10.3-2.fc38.x86_64.rpm      22 MB/s | 705 kB     00:00    
(114/136): openldap-2.6.3-1.fc38.x86_64.rpm     9.8 MB/s | 254 kB     00:00    
(115/136): p11-kit-0.24.1-3.fc37.x86_64.rpm      13 MB/s | 376 kB     00:00    
(116/136): openssl-libs-3.0.5-6.fc38.x86_64.rpm  45 MB/s | 2.1 MB     00:00    
(117/136): p11-kit-trust-0.24.1-3.fc37.x86_64.r 4.5 MB/s | 138 kB     00:00    
(118/136): publicsuffix-list-dafsa-20210518-5.f 2.9 MB/s |  58 kB     00:00    
(119/136): python3-3.11.0-1.fc38.x86_64.rpm     985 kB/s |  27 kB     00:00    
(120/136): python-setuptools-wheel-65.5.1-1.fc3  19 MB/s | 715 kB     00:00    
(121/136): python-pip-wheel-22.2.2-2.fc38.noarc  33 MB/s | 1.4 MB     00:00    
(122/136): python3-distro-1.8.0-1.fc38.noarch.r 2.1 MB/s |  49 kB     00:00    
(123/136): python3-dnf-4.14.0-1.fc38.noarch.rpm  12 MB/s | 607 kB     00:00    
(124/136): python3-dnf-plugins-core-4.3.1-1.fc3 5.8 MB/s | 277 kB     00:00    
(125/136): python3-hawkey-0.68.0-1.fc38.x86_64. 2.6 MB/s | 108 kB     00:00    
(126/136): python3-libdnf-0.68.0-1.fc38.x86_64.  12 MB/s | 818 kB     00:00    
(127/136): python3-rpm-4.18.0-6.fc38.x86_64.rpm 1.5 MB/s |  94 kB     00:00    
(128/136): python3-six-1.16.0-8.fc37.noarch.rpm 807 kB/s |  42 kB     00:00    
(129/136): rpm-4.18.0-6.fc38.x86_64.rpm         9.0 MB/s | 572 kB     00:00    
(130/136): rpm-build-libs-4.18.0-6.fc38.x86_64. 2.7 MB/s |  94 kB     00:00    
(131/136): rpm-libs-4.18.0-6.fc38.x86_64.rpm     13 MB/s | 320 kB     00:00    
(132/136): rpm-sign-libs-4.18.0-6.fc38.x86_64.r 744 kB/s |  27 kB     00:00    
(133/136): shadow-utils-4.13-1.fc38.x86_64.rpm   19 MB/s | 1.3 MB     00:00    
(134/136): systemd-libs-252.1-588.fc38.x86_64.r 8.5 MB/s | 631 kB     00:00    
(135/136): python3-libs-3.11.0-1.fc38.x86_64.rp  35 MB/s | 9.6 MB     00:00    
(136/136): zchunk-libs-1.2.3-1.fc38.x86_64.rpm  886 kB/s |  51 kB     00:00    
--------------------------------------------------------------------------------
Total                                            37 MB/s |  55 MB     00:01     
fedora                                          1.6 MB/s | 1.6 kB     00:00    
Importing GPG key 0xEB10B464:
 Userid     : "Fedora (38) <fedora-38-primary@fedoraproject.org>"
 Fingerprint: 6A51 BBAB BA3D 5467 B617 1221 809A 8D7C EB10 B464
 From       : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary
Key imported successfully
fedora                                          1.6 MB/s | 1.6 kB     00:00    
GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary (0xEB10B464) is already installed
fedora                                          1.6 MB/s | 1.6 kB     00:00    
Importing GPG key 0x5323552A:
 Userid     : "Fedora (37) <fedora-37-primary@fedoraproject.org>"
 Fingerprint: ACB5 EE4E 831C 74BB 7C16 8D27 F55A D3FB 5323 552A
 From       : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-37-primary
Key imported successfully
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Running scriptlet: filesystem-3.18-2.fc37.x86_64                          1/1 
  Preparing        :                                                        1/1 
  Installing       : libgcc-12.2.1-3.fc38.x86_64                          1/136 
  Running scriptlet: libgcc-12.2.1-3.fc38.x86_64                          1/136 
  Installing       : crypto-policies-20221110-1.git87a75f4.fc38.noarc     2/136 
  Running scriptlet: crypto-policies-20221110-1.git87a75f4.fc38.noarc     2/136 
  Installing       : tzdata-2022f-1.fc38.noarch                           3/136 
  Installing       : fedora-release-identity-basic-38-0.4.noarch          4/136 
  Installing       : python-setuptools-wheel-65.5.1-1.fc38.noarch         5/136 
  Installing       : publicsuffix-list-dafsa-20210518-5.fc37.noarch       6/136 
  Installing       : libssh-config-0.10.4-2.fc38.noarch                   7/136 
  Installing       : libreport-filesystem-2.17.6-1.fc38.noarch            8/136 
  Installing       : dnf-data-4.14.0-1.fc38.noarch                        9/136 
warning: /etc/dnf/dnf.conf created as /etc/dnf/dnf.conf.rpmnew

  Installing       : fedora-gpg-keys-38-0.3.noarch                       10/136 
  Installing       : fedora-release-38-0.4.noarch                        11/136 
  Installing       : fedora-release-common-38-0.4.noarch                 12/136 
  Installing       : fedora-repos-rawhide-38-0.3.noarch                  13/136 
  Installing       : fedora-repos-38-0.3.noarch                          14/136 
  Installing       : setup-2.14.2-1.fc38.noarch                          15/136 
warning: /etc/hosts created as /etc/hosts.rpmnew

  Running scriptlet: setup-2.14.2-1.fc38.noarch                          15/136 
  Installing       : filesystem-3.18-2.fc37.x86_64                       16/136 
  Installing       : basesystem-11-14.fc37.noarch                        17/136 
  Installing       : pcre2-syntax-10.40-1.fc38.1.noarch                  18/136 
  Installing       : ncurses-base-6.3-3.20220501.fc38.noarch             19/136 
  Installing       : ncurses-libs-6.3-3.20220501.fc38.x86_64             20/136 
  Running scriptlet: glibc-2.36.9000-13.fc38.x86_64                      21/136 
  Installing       : glibc-2.36.9000-13.fc38.x86_64                      21/136 
  Running scriptlet: glibc-2.36.9000-13.fc38.x86_64                      21/136 
  Installing       : bash-5.2.2-2.fc38.x86_64                            22/136 
  Running scriptlet: bash-5.2.2-2.fc38.x86_64                            22/136 
  Installing       : glibc-common-2.36.9000-13.fc38.x86_64               23/136 
  Installing       : glibc-minimal-langpack-2.36.9000-13.fc38.x86_64     24/136 
  Installing       : zlib-1.2.12-5.fc38.x86_64                           25/136 
  Installing       : bzip2-libs-1.0.8-12.fc38.x86_64                     26/136 
  Installing       : xz-libs-5.2.7-1.fc38.x86_64                         27/136 
  Installing       : libzstd-1.5.2-3.fc38.x86_64                         28/136 
  Installing       : sqlite-libs-3.39.4-1.fc38.x86_64                    29/136 
  Installing       : libcap-2.48-5.fc38.x86_64                           30/136 
  Installing       : gmp-1:6.2.1-3.fc38.x86_64                           31/136 
  Installing       : libgpg-error-1.46-1.fc38.x86_64                     32/136 
  Installing       : popt-1.19-1.fc38.x86_64                             33/136 
  Installing       : libxml2-2.10.3-2.fc38.x86_64                        34/136 
  Installing       : lua-libs-5.4.4-6.fc38.x86_64                        35/136 
  Installing       : libstdc++-12.2.1-3.fc38.x86_64                      36/136 
  Installing       : file-libs-5.42-4.fc38.x86_64                        37/136 
  Installing       : elfutils-libelf-0.188-3.fc38.x86_64                 38/136 
  Installing       : libattr-2.5.1-5.fc38.x86_64                         39/136 
  Installing       : libacl-2.3.1-4.fc38.x86_64                          40/136 
  Installing       : libunistring-1.0-2.fc38.x86_64                      41/136 
  Installing       : libidn2-2.3.4-1.fc38.x86_64                         42/136 
  Installing       : libuuid-2.38.1-2.fc38.x86_64                        43/136 
  Installing       : pcre2-10.40-1.fc38.1.x86_64                         44/136 
  Installing       : readline-8.2-2.fc38.x86_64                          45/136 
  Installing       : libffi-3.4.4-1.fc38.x86_64                          46/136 
  Installing       : p11-kit-0.24.1-3.fc37.x86_64                        47/136 
  Installing       : libxcrypt-4.4.30-3.fc38.x86_64                      48/136 
  Installing       : libassuan-2.5.5-5.fc38.x86_64                       49/136 
  Installing       : expat-2.4.8-2.fc38.x86_64                           50/136 
  Installing       : gdbm-libs-1:1.23-2.fc38.x86_64                      51/136 
  Installing       : keyutils-libs-1.6.1-5.fc38.x86_64                   52/136 
  Installing       : libcom_err-1.46.5-3.fc38.x86_64                     53/136 
  Installing       : libsepol-3.4-3.fc38.x86_64                          54/136 
  Installing       : libselinux-3.4-5.fc38.x86_64                        55/136 
  Installing       : sed-4.8-11.fc38.x86_64                              56/136 
  Installing       : libsmartcols-2.38.1-2.fc38.x86_64                   57/136 
  Installing       : libtasn1-4.18.0-3.fc38.x86_64                       58/136 
  Installing       : lz4-libs-1.9.3-5.fc38.x86_64                        59/136 
  Installing       : json-c-0.16-3.fc38.x86_64                           60/136 
  Installing       : libgomp-12.2.1-3.fc38.x86_64                        61/136 
  Installing       : libb2-0.98.1-7.fc38.x86_64                          62/136 
  Installing       : systemd-libs-252.1-588.fc38.x86_64                  63/136 
  Installing       : dbus-libs-1:1.14.4-1.fc38.x86_64                    64/136 
  Installing       : findutils-1:4.9.0-2.fc38.x86_64                     65/136 
  Installing       : cyrus-sasl-lib-2.1.28-8.fc38.x86_64                 66/136 
  Installing       : libcomps-0.1.18-4.fc38.x86_64                       67/136 
  Installing       : grep-3.8-1.fc38.x86_64                              68/136 
  Installing       : libblkid-2.38.1-2.fc38.x86_64                       69/136 
  Installing       : libmount-2.38.1-2.fc38.x86_64                       70/136 
  Installing       : libpsl-0.21.1-6.fc38.x86_64                         71/136 
  Installing       : mpdecimal-2.5.1-4.fc38.x86_64                       72/136 
  Installing       : libksba-1.6.2-1.fc38.x86_64                         73/136 
  Installing       : libgcrypt-1.10.1-5.fc38.x86_64                      74/136 
  Installing       : mpfr-4.1.0-10.fc38.x86_64                           75/136 
  Installing       : nettle-3.8-2.fc38.x86_64                            76/136 
  Installing       : elfutils-default-yama-scope-0.188-3.fc38.noarch     77/136 
  Running scriptlet: elfutils-default-yama-scope-0.188-3.fc38.noarch     77/136 
  Installing       : elfutils-libs-0.188-3.fc38.x86_64                   78/136 
  Installing       : alternatives-1.21-1.fc38.x86_64                     79/136 
  Installing       : p11-kit-trust-0.24.1-3.fc37.x86_64                  80/136 
  Running scriptlet: p11-kit-trust-0.24.1-3.fc37.x86_64                  80/136 
  Installing       : gnutls-3.7.8-9.fc38.x86_64                          81/136 
  Installing       : glib2-2.74.1-2.fc38.x86_64                          82/136 
  Installing       : libcap-ng-0.8.3-3.fc38.x86_64                       83/136 
  Installing       : audit-libs-3.0.9-1.fc38.x86_64                      84/136 
  Installing       : libsemanage-3.4-5.fc38.x86_64                       85/136 
  Installing       : shadow-utils-2:4.13-1.fc38.x86_64                   86/136 
  Installing       : libnghttp2-1.50.0-1.fc38.x86_64                     87/136 
  Installing       : libsigsegv-2.14-3.fc38.x86_64                       88/136 
  Installing       : gawk-5.1.1-4.fc38.x86_64                            89/136 
  Installing       : libverto-0.3.2-4.fc38.x86_64                        90/136 
  Installing       : libyaml-0.2.5-8.fc38.x86_64                         91/136 
  Installing       : npth-1.6-10.fc38.x86_64                             92/136 
  Installing       : libbrotli-1.0.9-9.fc37.x86_64                       93/136 
  Installing       : coreutils-common-9.1-8.fc38.x86_64                  94/136 
  Installing       : openssl-libs-1:3.0.5-6.fc38.x86_64                  95/136 
  Installing       : coreutils-9.1-8.fc38.x86_64                         96/136 
  Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch             97/136 
  Installing       : ca-certificates-2022.2.54-5.fc37.noarch             97/136 
  Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch             97/136 
  Installing       : rpm-libs-4.18.0-6.fc38.x86_64                       98/136 
  Installing       : krb5-libs-1.19.2-11.fc38.1.x86_64                   99/136 
  Installing       : libtirpc-1.3.3-0.fc38.x86_64                       100/136 
  Installing       : libmodulemd-2.14.0-4.fc37.x86_64                   101/136 
  Installing       : libfsverity-1.4-8.fc38.x86_64                      102/136 
  Installing       : zchunk-libs-1.2.3-1.fc38.x86_64                    103/136 
  Installing       : libsolv-0.7.22-3.fc37.x86_64                       104/136 
  Installing       : libnsl2-2.0.0-4.fc38.x86_64                        105/136 
  Installing       : libssh-0.10.4-2.fc38.x86_64                        106/136 
  Installing       : rpm-build-libs-4.18.0-6.fc38.x86_64                107/136 
  Installing       : python-pip-wheel-22.2.2-2.fc38.noarch              108/136 
  Installing       : python3-3.11.0-1.fc38.x86_64                       109/136 
  Installing       : python3-libs-3.11.0-1.fc38.x86_64                  110/136 
  Installing       : python3-dbus-1.3.2-1.fc38.x86_64                   111/136 
  Installing       : python3-libcomps-0.1.18-4.fc38.x86_64              112/136 
  Installing       : python3-distro-1.8.0-1.fc38.noarch                 113/136 
  Installing       : python3-six-1.16.0-8.fc37.noarch                   114/136 
  Installing       : python3-dateutil-1:2.8.2-4.fc38.noarch             115/136 
  Installing       : libarchive-3.6.1-2.fc38.x86_64                     116/136 
  Installing       : libevent-2.1.12-7.fc38.x86_64                      117/136 
  Installing       : openldap-2.6.3-1.fc38.x86_64                       118/136 
  Installing       : libcurl-7.86.0-2.fc38.x86_64                       119/136 
  Installing       : gnupg2-2.3.8-1.fc38.x86_64                         120/136 
  Installing       : gpgme-1.17.0-4.fc38.x86_64                         121/136 
  Installing       : python3-gpg-1.17.0-4.fc38.x86_64                   122/136 
  Installing       : librepo-1.14.4-1.fc38.x86_64                       123/136 
  Installing       : libdnf-0.68.0-1.fc38.x86_64                        124/136 
  Installing       : python3-libdnf-0.68.0-1.fc38.x86_64                125/136 
  Installing       : python3-hawkey-0.68.0-1.fc38.x86_64                126/136 
  Running scriptlet: tpm2-tss-3.2.0-3.fc38.x86_64                       127/136 
useradd: Warning: missing or non-executable shell '/usr/sbin/nologin'

  Installing       : tpm2-tss-3.2.0-3.fc38.x86_64                       127/136 
  Installing       : ima-evm-utils-1.4-6.fc38.x86_64                    128/136 
  Installing       : rpm-sign-libs-4.18.0-6.fc38.x86_64                 129/136 
  Installing       : python3-rpm-4.18.0-6.fc38.x86_64                   130/136 
  Installing       : python3-dnf-4.14.0-1.fc38.noarch                   131/136 
  Installing       : python3-dnf-plugins-core-4.3.1-1.fc38.noarch       132/136 
  Installing       : curl-7.86.0-2.fc38.x86_64                          133/136 
  Running scriptlet: rpm-4.18.0-6.fc38.x86_64                           134/136 
  Installing       : rpm-4.18.0-6.fc38.x86_64                           134/136 
  Installing       : dnf-plugins-core-4.3.1-1.fc38.noarch               135/136 
  Installing       : dnf-4.14.0-1.fc38.noarch                           136/136 
  Running scriptlet: dnf-4.14.0-1.fc38.noarch                           136/136 
  Running scriptlet: filesystem-3.18-2.fc37.x86_64                      136/136 
  Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch            136/136 
  Running scriptlet: rpm-4.18.0-6.fc38.x86_64                           136/136 
  Running scriptlet: dnf-4.14.0-1.fc38.noarch                           136/136 
  Verifying        : alternatives-1.21-1.fc38.x86_64                      1/136 
  Verifying        : audit-libs-3.0.9-1.fc38.x86_64                       2/136 
  Verifying        : bash-5.2.2-2.fc38.x86_64                             3/136 
  Verifying        : bzip2-libs-1.0.8-12.fc38.x86_64                      4/136 
  Verifying        : coreutils-9.1-8.fc38.x86_64                          5/136 
  Verifying        : coreutils-common-9.1-8.fc38.x86_64                   6/136 
  Verifying        : cyrus-sasl-lib-2.1.28-8.fc38.x86_64                  7/136 
  Verifying        : dbus-libs-1:1.14.4-1.fc38.x86_64                     8/136 
  Verifying        : expat-2.4.8-2.fc38.x86_64                            9/136 
  Verifying        : file-libs-5.42-4.fc38.x86_64                        10/136 
  Verifying        : findutils-1:4.9.0-2.fc38.x86_64                     11/136 
  Verifying        : gawk-5.1.1-4.fc38.x86_64                            12/136 
  Verifying        : gdbm-libs-1:1.23-2.fc38.x86_64                      13/136 
  Verifying        : gmp-1:6.2.1-3.fc38.x86_64                           14/136 
  Verifying        : gnupg2-2.3.8-1.fc38.x86_64                          15/136 
  Verifying        : gpgme-1.17.0-4.fc38.x86_64                          16/136 
  Verifying        : grep-3.8-1.fc38.x86_64                              17/136 
  Verifying        : ima-evm-utils-1.4-6.fc38.x86_64                     18/136 
  Verifying        : keyutils-libs-1.6.1-5.fc38.x86_64                   19/136 
  Verifying        : krb5-libs-1.19.2-11.fc38.1.x86_64                   20/136 
  Verifying        : libacl-2.3.1-4.fc38.x86_64                          21/136 
  Verifying        : libarchive-3.6.1-2.fc38.x86_64                      22/136 
  Verifying        : libassuan-2.5.5-5.fc38.x86_64                       23/136 
  Verifying        : libattr-2.5.1-5.fc38.x86_64                         24/136 
  Verifying        : libb2-0.98.1-7.fc38.x86_64                          25/136 
  Verifying        : libblkid-2.38.1-2.fc38.x86_64                       26/136 
  Verifying        : libcap-2.48-5.fc38.x86_64                           27/136 
  Verifying        : libcap-ng-0.8.3-3.fc38.x86_64                       28/136 
  Verifying        : libcom_err-1.46.5-3.fc38.x86_64                     29/136 
  Verifying        : libcomps-0.1.18-4.fc38.x86_64                       30/136 
  Verifying        : libevent-2.1.12-7.fc38.x86_64                       31/136 
  Verifying        : libfsverity-1.4-8.fc38.x86_64                       32/136 
  Verifying        : libgpg-error-1.46-1.fc38.x86_64                     33/136 
  Verifying        : libidn2-2.3.4-1.fc38.x86_64                         34/136 
  Verifying        : libksba-1.6.2-1.fc38.x86_64                         35/136 
  Verifying        : libmount-2.38.1-2.fc38.x86_64                       36/136 
  Verifying        : libnghttp2-1.50.0-1.fc38.x86_64                     37/136 
  Verifying        : libnsl2-2.0.0-4.fc38.x86_64                         38/136 
  Verifying        : libpsl-0.21.1-6.fc38.x86_64                         39/136 
  Verifying        : libselinux-3.4-5.fc38.x86_64                        40/136 
  Verifying        : libsemanage-3.4-5.fc38.x86_64                       41/136 
  Verifying        : libsepol-3.4-3.fc38.x86_64                          42/136 
  Verifying        : libsigsegv-2.14-3.fc38.x86_64                       43/136 
  Verifying        : libsmartcols-2.38.1-2.fc38.x86_64                   44/136 
  Verifying        : libtasn1-4.18.0-3.fc38.x86_64                       45/136 
  Verifying        : libtirpc-1.3.3-0.fc38.x86_64                        46/136 
  Verifying        : libunistring-1.0-2.fc38.x86_64                      47/136 
  Verifying        : libuuid-2.38.1-2.fc38.x86_64                        48/136 
  Verifying        : libverto-0.3.2-4.fc38.x86_64                        49/136 
  Verifying        : libyaml-0.2.5-8.fc38.x86_64                         50/136 
  Verifying        : libzstd-1.5.2-3.fc38.x86_64                         51/136 
  Verifying        : lua-libs-5.4.4-6.fc38.x86_64                        52/136 
  Verifying        : lz4-libs-1.9.3-5.fc38.x86_64                        53/136 
  Verifying        : mpdecimal-2.5.1-4.fc38.x86_64                       54/136 
  Verifying        : mpfr-4.1.0-10.fc38.x86_64                           55/136 
  Verifying        : ncurses-base-6.3-3.20220501.fc38.noarch             56/136 
  Verifying        : ncurses-libs-6.3-3.20220501.fc38.x86_64             57/136 
  Verifying        : nettle-3.8-2.fc38.x86_64                            58/136 
  Verifying        : npth-1.6-10.fc38.x86_64                             59/136 
  Verifying        : pcre2-10.40-1.fc38.1.x86_64                         60/136 
  Verifying        : pcre2-syntax-10.40-1.fc38.1.noarch                  61/136 
  Verifying        : popt-1.19-1.fc38.x86_64                             62/136 
  Verifying        : python3-dateutil-1:2.8.2-4.fc38.noarch              63/136 
  Verifying        : python3-dbus-1.3.2-1.fc38.x86_64                    64/136 
  Verifying        : python3-gpg-1.17.0-4.fc38.x86_64                    65/136 
  Verifying        : python3-libcomps-0.1.18-4.fc38.x86_64               66/136 
  Verifying        : readline-8.2-2.fc38.x86_64                          67/136 
  Verifying        : sed-4.8-11.fc38.x86_64                              68/136 
  Verifying        : setup-2.14.2-1.fc38.noarch                          69/136 
  Verifying        : sqlite-libs-3.39.4-1.fc38.x86_64                    70/136 
  Verifying        : tpm2-tss-3.2.0-3.fc38.x86_64                        71/136 
  Verifying        : tzdata-2022f-1.fc38.noarch                          72/136 
  Verifying        : xz-libs-5.2.7-1.fc38.x86_64                         73/136 
  Verifying        : zlib-1.2.12-5.fc38.x86_64                           74/136 
  Verifying        : basesystem-11-14.fc37.noarch                        75/136 
  Verifying        : ca-certificates-2022.2.54-5.fc37.noarch             76/136 
  Verifying        : crypto-policies-20221110-1.git87a75f4.fc38.noarc    77/136 
  Verifying        : curl-7.86.0-2.fc38.x86_64                           78/136 
  Verifying        : dnf-4.14.0-1.fc38.noarch                            79/136 
  Verifying        : dnf-data-4.14.0-1.fc38.noarch                       80/136 
  Verifying        : dnf-plugins-core-4.3.1-1.fc38.noarch                81/136 
  Verifying        : elfutils-default-yama-scope-0.188-3.fc38.noarch     82/136 
  Verifying        : elfutils-libelf-0.188-3.fc38.x86_64                 83/136 
  Verifying        : elfutils-libs-0.188-3.fc38.x86_64                   84/136 
  Verifying        : fedora-gpg-keys-38-0.3.noarch                       85/136 
  Verifying        : fedora-release-38-0.4.noarch                        86/136 
  Verifying        : fedora-release-common-38-0.4.noarch                 87/136 
  Verifying        : fedora-release-identity-basic-38-0.4.noarch         88/136 
  Verifying        : fedora-repos-38-0.3.noarch                          89/136 
  Verifying        : fedora-repos-rawhide-38-0.3.noarch                  90/136 
  Verifying        : filesystem-3.18-2.fc37.x86_64                       91/136 
  Verifying        : glib2-2.74.1-2.fc38.x86_64                          92/136 
  Verifying        : glibc-2.36.9000-13.fc38.x86_64                      93/136 
  Verifying        : glibc-common-2.36.9000-13.fc38.x86_64               94/136 
  Verifying        : glibc-minimal-langpack-2.36.9000-13.fc38.x86_64     95/136 
  Verifying        : gnutls-3.7.8-9.fc38.x86_64                          96/136 
  Verifying        : json-c-0.16-3.fc38.x86_64                           97/136 
  Verifying        : libbrotli-1.0.9-9.fc37.x86_64                       98/136 
  Verifying        : libcurl-7.86.0-2.fc38.x86_64                        99/136 
  Verifying        : libdnf-0.68.0-1.fc38.x86_64                        100/136 
  Verifying        : libffi-3.4.4-1.fc38.x86_64                         101/136 
  Verifying        : libgcc-12.2.1-3.fc38.x86_64                        102/136 
  Verifying        : libgcrypt-1.10.1-5.fc38.x86_64                     103/136 
  Verifying        : libgomp-12.2.1-3.fc38.x86_64                       104/136 
  Verifying        : libmodulemd-2.14.0-4.fc37.x86_64                   105/136 
  Verifying        : librepo-1.14.4-1.fc38.x86_64                       106/136 
  Verifying        : libreport-filesystem-2.17.6-1.fc38.noarch          107/136 
  Verifying        : libsolv-0.7.22-3.fc37.x86_64                       108/136 
  Verifying        : libssh-0.10.4-2.fc38.x86_64                        109/136 
  Verifying        : libssh-config-0.10.4-2.fc38.noarch                 110/136 
  Verifying        : libstdc++-12.2.1-3.fc38.x86_64                     111/136 
  Verifying        : libxcrypt-4.4.30-3.fc38.x86_64                     112/136 
  Verifying        : libxml2-2.10.3-2.fc38.x86_64                       113/136 
  Verifying        : openldap-2.6.3-1.fc38.x86_64                       114/136 
  Verifying        : openssl-libs-1:3.0.5-6.fc38.x86_64                 115/136 
  Verifying        : p11-kit-0.24.1-3.fc37.x86_64                       116/136 
  Verifying        : p11-kit-trust-0.24.1-3.fc37.x86_64                 117/136 
  Verifying        : publicsuffix-list-dafsa-20210518-5.fc37.noarch     118/136 
  Verifying        : python-pip-wheel-22.2.2-2.fc38.noarch              119/136 
  Verifying        : python-setuptools-wheel-65.5.1-1.fc38.noarch       120/136 
  Verifying        : python3-3.11.0-1.fc38.x86_64                       121/136 
  Verifying        : python3-distro-1.8.0-1.fc38.noarch                 122/136 
  Verifying        : python3-dnf-4.14.0-1.fc38.noarch                   123/136 
  Verifying        : python3-dnf-plugins-core-4.3.1-1.fc38.noarch       124/136 
  Verifying        : python3-hawkey-0.68.0-1.fc38.x86_64                125/136 
  Verifying        : python3-libdnf-0.68.0-1.fc38.x86_64                126/136 
  Verifying        : python3-libs-3.11.0-1.fc38.x86_64                  127/136 
  Verifying        : python3-rpm-4.18.0-6.fc38.x86_64                   128/136 
  Verifying        : python3-six-1.16.0-8.fc37.noarch                   129/136 
  Verifying        : rpm-4.18.0-6.fc38.x86_64                           130/136 
  Verifying        : rpm-build-libs-4.18.0-6.fc38.x86_64                131/136 
  Verifying        : rpm-libs-4.18.0-6.fc38.x86_64                      132/136 
  Verifying        : rpm-sign-libs-4.18.0-6.fc38.x86_64                 133/136 
  Verifying        : shadow-utils-2:4.13-1.fc38.x86_64                  134/136 
  Verifying        : systemd-libs-252.1-588.fc38.x86_64                 135/136 
  Verifying        : zchunk-libs-1.2.3-1.fc38.x86_64                    136/136 
Installed products updated.

Installed:
  alternatives-1.21-1.fc38.x86_64                                               
  audit-libs-3.0.9-1.fc38.x86_64                                                
  basesystem-11-14.fc37.noarch                                                  
  bash-5.2.2-2.fc38.x86_64                                                      
  bzip2-libs-1.0.8-12.fc38.x86_64                                               
  ca-certificates-2022.2.54-5.fc37.noarch                                       
  coreutils-9.1-8.fc38.x86_64                                                   
  coreutils-common-9.1-8.fc38.x86_64                                            
  crypto-policies-20221110-1.git87a75f4.fc38.noarch                             
  curl-7.86.0-2.fc38.x86_64                                                     
  cyrus-sasl-lib-2.1.28-8.fc38.x86_64                                           
  dbus-libs-1:1.14.4-1.fc38.x86_64                                              
  dnf-4.14.0-1.fc38.noarch                                                      
  dnf-data-4.14.0-1.fc38.noarch                                                 
  dnf-plugins-core-4.3.1-1.fc38.noarch                                          
  elfutils-default-yama-scope-0.188-3.fc38.noarch                               
  elfutils-libelf-0.188-3.fc38.x86_64                                           
  elfutils-libs-0.188-3.fc38.x86_64                                             
  expat-2.4.8-2.fc38.x86_64                                                     
  fedora-gpg-keys-38-0.3.noarch                                                 
  fedora-release-38-0.4.noarch                                                  
  fedora-release-common-38-0.4.noarch                                           
  fedora-release-identity-basic-38-0.4.noarch                                   
  fedora-repos-38-0.3.noarch                                                    
  fedora-repos-rawhide-38-0.3.noarch                                            
  file-libs-5.42-4.fc38.x86_64                                                  
  filesystem-3.18-2.fc37.x86_64                                                 
  findutils-1:4.9.0-2.fc38.x86_64                                               
  gawk-5.1.1-4.fc38.x86_64                                                      
  gdbm-libs-1:1.23-2.fc38.x86_64                                                
  glib2-2.74.1-2.fc38.x86_64                                                    
  glibc-2.36.9000-13.fc38.x86_64                                                
  glibc-common-2.36.9000-13.fc38.x86_64                                         
  glibc-minimal-langpack-2.36.9000-13.fc38.x86_64                               
  gmp-1:6.2.1-3.fc38.x86_64                                                     
  gnupg2-2.3.8-1.fc38.x86_64                                                    
  gnutls-3.7.8-9.fc38.x86_64                                                    
  gpgme-1.17.0-4.fc38.x86_64                                                    
  grep-3.8-1.fc38.x86_64                                                        
  ima-evm-utils-1.4-6.fc38.x86_64                                               
  json-c-0.16-3.fc38.x86_64                                                     
  keyutils-libs-1.6.1-5.fc38.x86_64                                             
  krb5-libs-1.19.2-11.fc38.1.x86_64                                             
  libacl-2.3.1-4.fc38.x86_64                                                    
  libarchive-3.6.1-2.fc38.x86_64                                                
  libassuan-2.5.5-5.fc38.x86_64                                                 
  libattr-2.5.1-5.fc38.x86_64                                                   
  libb2-0.98.1-7.fc38.x86_64                                                    
  libblkid-2.38.1-2.fc38.x86_64                                                 
  libbrotli-1.0.9-9.fc37.x86_64                                                 
  libcap-2.48-5.fc38.x86_64                                                     
  libcap-ng-0.8.3-3.fc38.x86_64                                                 
  libcom_err-1.46.5-3.fc38.x86_64                                               
  libcomps-0.1.18-4.fc38.x86_64                                                 
  libcurl-7.86.0-2.fc38.x86_64                                                  
  libdnf-0.68.0-1.fc38.x86_64                                                   
  libevent-2.1.12-7.fc38.x86_64                                                 
  libffi-3.4.4-1.fc38.x86_64                                                    
  libfsverity-1.4-8.fc38.x86_64                                                 
  libgcc-12.2.1-3.fc38.x86_64                                                   
  libgcrypt-1.10.1-5.fc38.x86_64                                                
  libgomp-12.2.1-3.fc38.x86_64                                                  
  libgpg-error-1.46-1.fc38.x86_64                                               
  libidn2-2.3.4-1.fc38.x86_64                                                   
  libksba-1.6.2-1.fc38.x86_64                                                   
  libmodulemd-2.14.0-4.fc37.x86_64                                              
  libmount-2.38.1-2.fc38.x86_64                                                 
  libnghttp2-1.50.0-1.fc38.x86_64                                               
  libnsl2-2.0.0-4.fc38.x86_64                                                   
  libpsl-0.21.1-6.fc38.x86_64                                                   
  librepo-1.14.4-1.fc38.x86_64                                                  
  libreport-filesystem-2.17.6-1.fc38.noarch                                     
  libselinux-3.4-5.fc38.x86_64                                                  
  libsemanage-3.4-5.fc38.x86_64                                                 
  libsepol-3.4-3.fc38.x86_64                                                    
  libsigsegv-2.14-3.fc38.x86_64                                                 
  libsmartcols-2.38.1-2.fc38.x86_64                                             
  libsolv-0.7.22-3.fc37.x86_64                                                  
  libssh-0.10.4-2.fc38.x86_64                                                   
  libssh-config-0.10.4-2.fc38.noarch                                            
  libstdc++-12.2.1-3.fc38.x86_64                                                
  libtasn1-4.18.0-3.fc38.x86_64                                                 
  libtirpc-1.3.3-0.fc38.x86_64                                                  
  libunistring-1.0-2.fc38.x86_64                                                
  libuuid-2.38.1-2.fc38.x86_64                                                  
  libverto-0.3.2-4.fc38.x86_64                                                  
  libxcrypt-4.4.30-3.fc38.x86_64                                                
  libxml2-2.10.3-2.fc38.x86_64                                                  
  libyaml-0.2.5-8.fc38.x86_64                                                   
  libzstd-1.5.2-3.fc38.x86_64                                                   
  lua-libs-5.4.4-6.fc38.x86_64                                                  
  lz4-libs-1.9.3-5.fc38.x86_64                                                  
  mpdecimal-2.5.1-4.fc38.x86_64                                                 
  mpfr-4.1.0-10.fc38.x86_64                                                     
  ncurses-base-6.3-3.20220501.fc38.noarch                                       
  ncurses-libs-6.3-3.20220501.fc38.x86_64                                       
  nettle-3.8-2.fc38.x86_64                                                      
  npth-1.6-10.fc38.x86_64                                                       
  openldap-2.6.3-1.fc38.x86_64                                                  
  openssl-libs-1:3.0.5-6.fc38.x86_64                                            
  p11-kit-0.24.1-3.fc37.x86_64                                                  
  p11-kit-trust-0.24.1-3.fc37.x86_64                                            
  pcre2-10.40-1.fc38.1.x86_64                                                   
  pcre2-syntax-10.40-1.fc38.1.noarch                                            
  popt-1.19-1.fc38.x86_64                                                       
  publicsuffix-list-dafsa-20210518-5.fc37.noarch                                
  python-pip-wheel-22.2.2-2.fc38.noarch                                         
  python-setuptools-wheel-65.5.1-1.fc38.noarch                                  
  python3-3.11.0-1.fc38.x86_64                                                  
  python3-dateutil-1:2.8.2-4.fc38.noarch                                        
  python3-dbus-1.3.2-1.fc38.x86_64                                              
  python3-distro-1.8.0-1.fc38.noarch                                            
  python3-dnf-4.14.0-1.fc38.noarch                                              
  python3-dnf-plugins-core-4.3.1-1.fc38.noarch                                  
  python3-gpg-1.17.0-4.fc38.x86_64                                              
  python3-hawkey-0.68.0-1.fc38.x86_64                                           
  python3-libcomps-0.1.18-4.fc38.x86_64                                         
  python3-libdnf-0.68.0-1.fc38.x86_64                                           
  python3-libs-3.11.0-1.fc38.x86_64                                             
  python3-rpm-4.18.0-6.fc38.x86_64                                              
  python3-six-1.16.0-8.fc37.noarch                                              
  readline-8.2-2.fc38.x86_64                                                    
  rpm-4.18.0-6.fc38.x86_64                                                      
  rpm-build-libs-4.18.0-6.fc38.x86_64                                           
  rpm-libs-4.18.0-6.fc38.x86_64                                                 
  rpm-sign-libs-4.18.0-6.fc38.x86_64                                            
  sed-4.8-11.fc38.x86_64                                                        
  setup-2.14.2-1.fc38.noarch                                                    
  shadow-utils-2:4.13-1.fc38.x86_64                                             
  sqlite-libs-3.39.4-1.fc38.x86_64                                              
  systemd-libs-252.1-588.fc38.x86_64                                            
  tpm2-tss-3.2.0-3.fc38.x86_64                                                  
  tzdata-2022f-1.fc38.noarch                                                    
  xz-libs-5.2.7-1.fc38.x86_64                                                   
  zchunk-libs-1.2.3-1.fc38.x86_64                                               
  zlib-1.2.12-5.fc38.x86_64                                                     

Complete!
Finish(bootstrap): dnf install
Start(bootstrap): creating root cache
Finish(bootstrap): creating root cache
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1668321698.617486/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
Mock Version: 3.3
INFO: Mock Version: 3.3
Start: dnf install
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                  63 MB/s |  34 MB     00:00    
fedora                                           14 MB/s |  65 MB     00:04    
Last metadata expiration check: 0:00:07 ago on Sun Nov 13 06:42:39 2022.
Dependencies resolved.
================================================================================
 Package                      Arch   Version                    Repo       Size
================================================================================
Installing group/module packages:
 bash                         x86_64 5.2.2-2.fc38               copr_base 1.8 M
 bzip2                        x86_64 1.0.8-12.fc38              copr_base  53 k
 coreutils                    x86_64 9.1-8.fc38                 copr_base 1.1 M
 cpio                         x86_64 2.13-13.fc38               copr_base 270 k
 diffutils                    x86_64 3.8-3.fc37                 fedora    378 k
 fedora-release-common        noarch 38-0.4                     fedora     22 k
 findutils                    x86_64 1:4.9.0-2.fc38             copr_base 483 k
 gawk                         x86_64 5.1.1-4.fc38               copr_base 1.0 M
 glibc-minimal-langpack       x86_64 2.36.9000-13.fc38          fedora     25 k
 grep                         x86_64 3.8-1.fc38                 copr_base 282 k
 gzip                         x86_64 1.12-2.fc38                copr_base 159 k
 info                         x86_64 6.8-4.fc38                 copr_base 225 k
 patch                        x86_64 2.7.6-17.fc38              copr_base 124 k
 redhat-rpm-config            noarch 233-1.fc38                 fedora     81 k
 rpm-build                    x86_64 4.18.0-6.fc38              fedora     77 k
 sed                          x86_64 4.8-11.fc38                copr_base 297 k
 shadow-utils                 x86_64 2:4.13-1.fc38              fedora    1.3 M
 tar                          x86_64 2:1.34-5.fc38              fedora    885 k
 unzip                        x86_64 6.0-58.fc38                copr_base 183 k
 util-linux                   x86_64 2.38.1-2.fc38              copr_base 2.3 M
 which                        x86_64 2.21-36.fc38               fedora     41 k
 xz                           x86_64 5.2.7-1.fc38               copr_base 294 k
Installing dependencies:
 alternatives                 x86_64 1.21-1.fc38                copr_base  38 k
 ansible-srpm-macros          noarch 1-8.1.fc38                 fedora    8.6 k
 audit-libs                   x86_64 3.0.9-1.fc38               copr_base 116 k
 authselect                   x86_64 1.4.0-3.fc37               fedora    144 k
 authselect-libs              x86_64 1.4.0-3.fc37               fedora    248 k
 basesystem                   noarch 11-14.fc37                 fedora    7.0 k
 binutils                     x86_64 2.39-5.fc38                fedora    5.4 M
 binutils-gold                x86_64 2.39-5.fc38                fedora    777 k
 bzip2-libs                   x86_64 1.0.8-12.fc38              copr_base  42 k
 ca-certificates              noarch 2022.2.54-5.fc37           fedora    829 k
 coreutils-common             x86_64 9.1-8.fc38                 copr_base 2.0 M
 cracklib                     x86_64 2.9.7-30.fc38              copr_base  81 k
 crypto-policies              noarch 20221110-1.git87a75f4.fc38 fedora     90 k
 curl                         x86_64 7.86.0-2.fc38              fedora    334 k
 cyrus-sasl-lib               x86_64 2.1.28-8.fc38              copr_base 794 k
 debugedit                    x86_64 5.0-5.fc38                 copr_base  77 k
 dwz                          x86_64 0.15-1.fc38                fedora    136 k
 ed                           x86_64 1.18-2.fc38                copr_base  79 k
 efi-srpm-macros              noarch 5-6.fc38                   copr_base  23 k
 elfutils                     x86_64 0.188-3.fc38               fedora    529 k
 elfutils-debuginfod-client   x86_64 0.188-3.fc38               fedora     40 k
 elfutils-default-yama-scope  noarch 0.188-3.fc38               fedora     15 k
 elfutils-libelf              x86_64 0.188-3.fc38               fedora    196 k
 elfutils-libs                x86_64 0.188-3.fc38               fedora    257 k
 fedora-gpg-keys              noarch 38-0.3                     fedora    125 k
 fedora-release               noarch 38-0.4                     fedora     11 k
 fedora-release-identity-basic
                              noarch 38-0.4                     fedora     12 k
 fedora-repos                 noarch 38-0.3                     fedora     10 k
 fedora-repos-rawhide         noarch 38-0.3                     fedora    9.7 k
 file                         x86_64 5.42-4.fc38                copr_base  49 k
 file-libs                    x86_64 5.42-4.fc38                copr_base 676 k
 filesystem                   x86_64 3.18-2.fc37                fedora    1.1 M
 fonts-srpm-macros            noarch 1:2.0.5-9.fc38             fedora     26 k
 fpc-srpm-macros              noarch 1.3-6.fc37                 fedora    7.7 k
 gdb-minimal                  x86_64 12.1-9.fc38                fedora    3.7 M
 gdbm-libs                    x86_64 1:1.23-2.fc38              copr_base  56 k
 ghc-srpm-macros              noarch 1.5.0-7.fc37               fedora    7.8 k
 glibc                        x86_64 2.36.9000-13.fc38          fedora    2.1 M
 glibc-common                 x86_64 2.36.9000-13.fc38          fedora    304 k
 glibc-gconv-extra            x86_64 2.36.9000-13.fc38          fedora    1.6 M
 gmp                          x86_64 1:6.2.1-3.fc38             copr_base 316 k
 gnat-srpm-macros             noarch 4-16.fc37                  fedora    8.3 k
 go-srpm-macros               noarch 3.2.0-1.fc38               fedora     27 k
 jansson                      x86_64 2.13.1-5.fc38              copr_base  45 k
 kernel-srpm-macros           noarch 1.0-15.fc37                fedora    9.4 k
 keyutils-libs                x86_64 1.6.1-5.fc38               copr_base  32 k
 krb5-libs                    x86_64 1.19.2-11.fc38.1           copr_base 724 k
 libacl                       x86_64 2.3.1-4.fc38               copr_base  24 k
 libarchive                   x86_64 3.6.1-2.fc38               copr_base 397 k
 libattr                      x86_64 2.5.1-5.fc38               copr_base  18 k
 libblkid                     x86_64 2.38.1-2.fc38              copr_base 107 k
 libbrotli                    x86_64 1.0.9-9.fc37               fedora    315 k
 libcap                       x86_64 2.48-5.fc38                copr_base  67 k
 libcap-ng                    x86_64 0.8.3-3.fc38               copr_base  33 k
 libcom_err                   x86_64 1.46.5-3.fc38              copr_base  26 k
 libcurl                      x86_64 7.86.0-2.fc38              fedora    305 k
 libdb                        x86_64 5.3.28-53.fc37             fedora    760 k
 libeconf                     x86_64 0.4.0-4.fc38               copr_base  28 k
 libevent                     x86_64 2.1.12-7.fc38              copr_base 259 k
 libfdisk                     x86_64 2.38.1-2.fc38              copr_base 161 k
 libffi                       x86_64 3.4.4-1.fc38               fedora     38 k
 libgcc                       x86_64 12.2.1-3.fc38              fedora    108 k
 libgomp                      x86_64 12.2.1-3.fc38              fedora    295 k
 libidn2                      x86_64 2.3.4-1.fc38               copr_base 154 k
 libmount                     x86_64 2.38.1-2.fc38              copr_base 136 k
 libnghttp2                   x86_64 1.50.0-1.fc38              copr_base  75 k
 libnsl2                      x86_64 2.0.0-4.fc38               copr_base  31 k
 libpkgconf                   x86_64 1.8.0-3.fc38               copr_base  36 k
 libpsl                       x86_64 0.21.1-6.fc38              copr_base  64 k
 libpwquality                 x86_64 1.4.4-11.fc38              copr_base 105 k
 libselinux                   x86_64 3.4-5.fc38                 copr_base  86 k
 libsemanage                  x86_64 3.4-5.fc38                 copr_base 120 k
 libsepol                     x86_64 3.4-3.fc38                 copr_base 322 k
 libsigsegv                   x86_64 2.14-3.fc38                copr_base  27 k
 libsmartcols                 x86_64 2.38.1-2.fc38              copr_base  65 k
 libssh                       x86_64 0.10.4-2.fc38              fedora    209 k
 libssh-config                noarch 0.10.4-2.fc38              fedora    8.8 k
 libstdc++                    x86_64 12.2.1-3.fc38              fedora    799 k
 libtasn1                     x86_64 4.18.0-3.fc38              copr_base  75 k
 libtirpc                     x86_64 1.3.3-0.fc38               copr_base  94 k
 libunistring                 x86_64 1.0-2.fc38                 copr_base 549 k
 libutempter                  x86_64 1.2.1-7.fc38               copr_base  26 k
 libuuid                      x86_64 2.38.1-2.fc38              copr_base  28 k
 libverto                     x86_64 0.3.2-4.fc38               copr_base  21 k
 libxcrypt                    x86_64 4.4.30-3.fc38              fedora    118 k
 libxml2                      x86_64 2.10.3-2.fc38              fedora    705 k
 libzstd                      x86_64 1.5.2-3.fc38               copr_base 295 k
 lua-libs                     x86_64 5.4.4-6.fc38               copr_base 132 k
 lua-srpm-macros              noarch 1-7.fc37                   fedora    8.8 k
 lz4-libs                     x86_64 1.9.3-5.fc38               copr_base  71 k
 mpfr                         x86_64 4.1.0-10.fc38              copr_base 331 k
 ncurses-base                 noarch 6.3-3.20220501.fc38        copr_base  62 k
 ncurses-libs                 x86_64 6.3-3.20220501.fc38        copr_base 329 k
 nim-srpm-macros              noarch 3-7.fc37                   fedora    8.4 k
 ocaml-srpm-macros            noarch 7-2.fc37                   fedora     13 k
 openblas-srpm-macros         noarch 2-12.fc37                  fedora    7.5 k
 openldap                     x86_64 2.6.3-1.fc38               fedora    254 k
 openssl-libs                 x86_64 1:3.0.5-6.fc38             fedora    2.1 M
 p11-kit                      x86_64 0.24.1-3.fc37              fedora    376 k
 p11-kit-trust                x86_64 0.24.1-3.fc37              fedora    138 k
 package-notes-srpm-macros    noarch 0.5-6.fc38                 fedora     11 k
 pam                          x86_64 1.5.2-14.fc37              fedora    560 k
 pam-libs                     x86_64 1.5.2-14.fc37              fedora     58 k
 pcre2                        x86_64 10.40-1.fc38.1             copr_base 237 k
 pcre2-syntax                 noarch 10.40-1.fc38.1             copr_base 143 k
 perl-srpm-macros             noarch 1-46.fc37                  fedora    8.3 k
 pkgconf                      x86_64 1.8.0-3.fc38               copr_base  42 k
 pkgconf-m4                   noarch 1.8.0-3.fc38               copr_base  15 k
 pkgconf-pkg-config           x86_64 1.8.0-3.fc38               copr_base  11 k
 popt                         x86_64 1.19-1.fc38                copr_base  59 k
 publicsuffix-list-dafsa      noarch 20210518-5.fc37            fedora     58 k
 python-srpm-macros           noarch 3.11-5.fc38                fedora     24 k
 qt5-srpm-macros              noarch 5.15.7-1.fc38              fedora    7.9 k
 readline                     x86_64 8.2-2.fc38                 copr_base 211 k
 rpm                          x86_64 4.18.0-6.fc38              fedora    572 k
 rpm-build-libs               x86_64 4.18.0-6.fc38              fedora     94 k
 rpm-libs                     x86_64 4.18.0-6.fc38              fedora    320 k
 rpmautospec-rpm-macros       noarch 0.3.1-1.fc38               fedora    8.8 k
 rust-srpm-macros             noarch 23-1.fc38                  fedora    9.4 k
 setup                        noarch 2.14.2-1.fc38              copr_base 145 k
 sqlite-libs                  x86_64 3.39.4-1.fc38              copr_base 659 k
 systemd-libs                 x86_64 252.1-588.fc38             fedora    631 k
 tzdata                       noarch 2022f-1.fc38               copr_base 431 k
 util-linux-core              x86_64 2.38.1-2.fc38              copr_base 455 k
 xxhash-libs                  x86_64 0.8.1-3.fc38               copr_base  41 k
 xz-libs                      x86_64 5.2.7-1.fc38               copr_base  93 k
 zip                          x86_64 3.0-33.fc38                copr_base 260 k
 zlib                         x86_64 1.2.12-5.fc38              copr_base  94 k
 zstd                         x86_64 1.5.2-3.fc38               copr_base 448 k
Installing Groups:
 Buildsystem building group                                                    

Transaction Summary
================================================================================
Install  151 Packages

Total download size: 51 M
Installed size: 177 M
Downloading Packages:
(1/151): alternatives-1.21-1.fc38.x86_64.rpm    388 kB/s |  38 kB     00:00    
(2/151): audit-libs-3.0.9-1.fc38.x86_64.rpm     1.0 MB/s | 116 kB     00:00    
(3/151): bzip2-1.0.8-12.fc38.x86_64.rpm         4.3 MB/s |  53 kB     00:00    
(4/151): bzip2-libs-1.0.8-12.fc38.x86_64.rpm    4.0 MB/s |  42 kB     00:00    
(5/151): bash-5.2.2-2.fc38.x86_64.rpm            11 MB/s | 1.8 MB     00:00    
(6/151): coreutils-9.1-8.fc38.x86_64.rpm         21 MB/s | 1.1 MB     00:00    
(7/151): coreutils-common-9.1-8.fc38.x86_64.rpm  29 MB/s | 2.0 MB     00:00    
(8/151): cpio-2.13-13.fc38.x86_64.rpm           7.6 MB/s | 270 kB     00:00    
(9/151): cracklib-2.9.7-30.fc38.x86_64.rpm      2.6 MB/s |  81 kB     00:00    
(10/151): cyrus-sasl-lib-2.1.28-8.fc38.x86_64.r  48 MB/s | 794 kB     00:00    
(11/151): ed-1.18-2.fc38.x86_64.rpm             5.3 MB/s |  79 kB     00:00    
(12/151): debugedit-5.0-5.fc38.x86_64.rpm       4.8 MB/s |  77 kB     00:00    
(13/151): efi-srpm-macros-5-6.fc38.noarch.rpm   2.4 MB/s |  23 kB     00:00    
(14/151): file-5.42-4.fc38.x86_64.rpm           5.1 MB/s |  49 kB     00:00    
(15/151): file-libs-5.42-4.fc38.x86_64.rpm       43 MB/s | 676 kB     00:00    
(16/151): findutils-4.9.0-2.fc38.x86_64.rpm      36 MB/s | 483 kB     00:00    
(17/151): gawk-5.1.1-4.fc38.x86_64.rpm           45 MB/s | 1.0 MB     00:00    
(18/151): gdbm-libs-1.23-2.fc38.x86_64.rpm      3.3 MB/s |  56 kB     00:00    
(19/151): gmp-6.2.1-3.fc38.x86_64.rpm            25 MB/s | 316 kB     00:00    
(20/151): grep-3.8-1.fc38.x86_64.rpm             26 MB/s | 282 kB     00:00    
(21/151): info-6.8-4.fc38.x86_64.rpm             19 MB/s | 225 kB     00:00    
(22/151): gzip-1.12-2.fc38.x86_64.rpm            11 MB/s | 159 kB     00:00    
(23/151): jansson-2.13.1-5.fc38.x86_64.rpm      4.9 MB/s |  45 kB     00:00    
(24/151): keyutils-libs-1.6.1-5.fc38.x86_64.rpm 3.8 MB/s |  32 kB     00:00    
(25/151): krb5-libs-1.19.2-11.fc38.1.x86_64.rpm  46 MB/s | 724 kB     00:00    
(26/151): libacl-2.3.1-4.fc38.x86_64.rpm        2.3 MB/s |  24 kB     00:00    
(27/151): libarchive-3.6.1-2.fc38.x86_64.rpm     33 MB/s | 397 kB     00:00    
(28/151): libattr-2.5.1-5.fc38.x86_64.rpm       2.0 MB/s |  18 kB     00:00    
(29/151): libblkid-2.38.1-2.fc38.x86_64.rpm      11 MB/s | 107 kB     00:00    
(30/151): libcap-2.48-5.fc38.x86_64.rpm         7.7 MB/s |  67 kB     00:00    
(31/151): libcap-ng-0.8.3-3.fc38.x86_64.rpm     3.8 MB/s |  33 kB     00:00    
(32/151): libcom_err-1.46.5-3.fc38.x86_64.rpm   3.1 MB/s |  26 kB     00:00    
(33/151): libeconf-0.4.0-4.fc38.x86_64.rpm      3.1 MB/s |  28 kB     00:00    
(34/151): libevent-2.1.12-7.fc38.x86_64.rpm      24 MB/s | 259 kB     00:00    
(35/151): libfdisk-2.38.1-2.fc38.x86_64.rpm      14 MB/s | 161 kB     00:00    
(36/151): libidn2-2.3.4-1.fc38.x86_64.rpm        16 MB/s | 154 kB     00:00    
(37/151): libmount-2.38.1-2.fc38.x86_64.rpm      14 MB/s | 136 kB     00:00    
(38/151): libnghttp2-1.50.0-1.fc38.x86_64.rpm   8.5 MB/s |  75 kB     00:00    
(39/151): libnsl2-2.0.0-4.fc38.x86_64.rpm       3.7 MB/s |  31 kB     00:00    
(40/151): libpsl-0.21.1-6.fc38.x86_64.rpm       7.3 MB/s |  64 kB     00:00    
(41/151): libpkgconf-1.8.0-3.fc38.x86_64.rpm    3.7 MB/s |  36 kB     00:00    
(42/151): libpwquality-1.4.4-11.fc38.x86_64.rpm  11 MB/s | 105 kB     00:00    
(43/151): libselinux-3.4-5.fc38.x86_64.rpm      9.2 MB/s |  86 kB     00:00    
(44/151): libsemanage-3.4-5.fc38.x86_64.rpm      12 MB/s | 120 kB     00:00    
(45/151): libsepol-3.4-3.fc38.x86_64.rpm         27 MB/s | 322 kB     00:00    
(46/151): libsigsegv-2.14-3.fc38.x86_64.rpm     3.2 MB/s |  27 kB     00:00    
(47/151): libsmartcols-2.38.1-2.fc38.x86_64.rpm 7.4 MB/s |  65 kB     00:00    
(48/151): libtasn1-4.18.0-3.fc38.x86_64.rpm     8.6 MB/s |  75 kB     00:00    
(49/151): libtirpc-1.3.3-0.fc38.x86_64.rpm       10 MB/s |  94 kB     00:00    
(50/151): libunistring-1.0-2.fc38.x86_64.rpm     40 MB/s | 549 kB     00:00    
(51/151): libutempter-1.2.1-7.fc38.x86_64.rpm   2.4 MB/s |  26 kB     00:00    
(52/151): libuuid-2.38.1-2.fc38.x86_64.rpm      3.4 MB/s |  28 kB     00:00    
(53/151): libverto-0.3.2-4.fc38.x86_64.rpm      2.6 MB/s |  21 kB     00:00    
(54/151): libzstd-1.5.2-3.fc38.x86_64.rpm        26 MB/s | 295 kB     00:00    
(55/151): lua-libs-5.4.4-6.fc38.x86_64.rpm       13 MB/s | 132 kB     00:00    
(56/151): lz4-libs-1.9.3-5.fc38.x86_64.rpm      7.8 MB/s |  71 kB     00:00    
(57/151): mpfr-4.1.0-10.fc38.x86_64.rpm          18 MB/s | 331 kB     00:00    
(58/151): ncurses-base-6.3-3.20220501.fc38.noar 3.3 MB/s |  62 kB     00:00    
(59/151): ncurses-libs-6.3-3.20220501.fc38.x86_  20 MB/s | 329 kB     00:00    
(60/151): pcre2-10.40-1.fc38.1.x86_64.rpm        23 MB/s | 237 kB     00:00    
(61/151): patch-2.7.6-17.fc38.x86_64.rpm         10 MB/s | 124 kB     00:00    
(62/151): pcre2-syntax-10.40-1.fc38.1.noarch.rp  13 MB/s | 143 kB     00:00    
(63/151): pkgconf-1.8.0-3.fc38.x86_64.rpm       4.5 MB/s |  42 kB     00:00    
(64/151): pkgconf-m4-1.8.0-3.fc38.noarch.rpm    1.6 MB/s |  15 kB     00:00    
(65/151): pkgconf-pkg-config-1.8.0-3.fc38.x86_6 1.2 MB/s |  11 kB     00:00    
(66/151): popt-1.19-1.fc38.x86_64.rpm           6.8 MB/s |  59 kB     00:00    
(67/151): readline-8.2-2.fc38.x86_64.rpm         20 MB/s | 211 kB     00:00    
(68/151): sed-4.8-11.fc38.x86_64.rpm             24 MB/s | 297 kB     00:00    
(69/151): setup-2.14.2-1.fc38.noarch.rpm         15 MB/s | 145 kB     00:00    
(70/151): sqlite-libs-3.39.4-1.fc38.x86_64.rpm   45 MB/s | 659 kB     00:00    
(71/151): tzdata-2022f-1.fc38.noarch.rpm         29 MB/s | 431 kB     00:00    
(72/151): unzip-6.0-58.fc38.x86_64.rpm           14 MB/s | 183 kB     00:00    
(73/151): xxhash-libs-0.8.1-3.fc38.x86_64.rpm   1.3 MB/s |  41 kB     00:00    
(74/151): util-linux-core-2.38.1-2.fc38.x86_64.  12 MB/s | 455 kB     00:00    
(75/151): util-linux-2.38.1-2.fc38.x86_64.rpm    52 MB/s | 2.3 MB     00:00    
(76/151): xz-5.2.7-1.fc38.x86_64.rpm             25 MB/s | 294 kB     00:00    
(77/151): xz-libs-5.2.7-1.fc38.x86_64.rpm        10 MB/s |  93 kB     00:00    
(78/151): zip-3.0-33.fc38.x86_64.rpm             21 MB/s | 260 kB     00:00    
(79/151): zlib-1.2.12-5.fc38.x86_64.rpm          10 MB/s |  94 kB     00:00    
(80/151): zstd-1.5.2-3.fc38.x86_64.rpm           34 MB/s | 448 kB     00:00    
(81/151): ansible-srpm-macros-1-8.1.fc38.noarch 114 kB/s | 8.6 kB     00:00    
(82/151): basesystem-11-14.fc37.noarch.rpm      339 kB/s | 7.0 kB     00:00    
(83/151): authselect-1.4.0-3.fc37.x86_64.rpm    942 kB/s | 144 kB     00:00    
(84/151): authselect-libs-1.4.0-3.fc37.x86_64.r 1.5 MB/s | 248 kB     00:00    
(85/151): binutils-gold-2.39-5.fc38.x86_64.rpm   12 MB/s | 777 kB     00:00    
(86/151): crypto-policies-20221110-1.git87a75f4 4.5 MB/s |  90 kB     00:00    
(87/151): curl-7.86.0-2.fc38.x86_64.rpm          14 MB/s | 334 kB     00:00    
(88/151): diffutils-3.8-3.fc37.x86_64.rpm        16 MB/s | 378 kB     00:00    
(89/151): dwz-0.15-1.fc38.x86_64.rpm            6.4 MB/s | 136 kB     00:00    
(90/151): ca-certificates-2022.2.54-5.fc37.noar 5.4 MB/s | 829 kB     00:00    
(91/151): elfutils-0.188-3.fc38.x86_64.rpm       20 MB/s | 529 kB     00:00    
(92/151): elfutils-debuginfod-client-0.188-3.fc 1.9 MB/s |  40 kB     00:00    
(93/151): elfutils-default-yama-scope-0.188-3.f 698 kB/s |  15 kB     00:00    
(94/151): elfutils-libs-0.188-3.fc38.x86_64.rpm  11 MB/s | 257 kB     00:00    
(95/151): elfutils-libelf-0.188-3.fc38.x86_64.r 4.5 MB/s | 196 kB     00:00    
(96/151): binutils-2.39-5.fc38.x86_64.rpm        18 MB/s | 5.4 MB     00:00    
(97/151): fedora-gpg-keys-38-0.3.noarch.rpm     5.1 MB/s | 125 kB     00:00    
(98/151): fedora-release-38-0.4.noarch.rpm      590 kB/s |  11 kB     00:00    
(99/151): fedora-release-identity-basic-38-0.4. 612 kB/s |  12 kB     00:00    
(100/151): fedora-release-common-38-0.4.noarch. 968 kB/s |  22 kB     00:00    
(101/151): fedora-repos-38-0.3.noarch.rpm       483 kB/s |  10 kB     00:00    
(102/151): fedora-repos-rawhide-38-0.3.noarch.r 515 kB/s | 9.7 kB     00:00    
(103/151): fonts-srpm-macros-2.0.5-9.fc38.noarc 1.1 MB/s |  26 kB     00:00    
(104/151): fpc-srpm-macros-1.3-6.fc37.noarch.rp 298 kB/s | 7.7 kB     00:00    
(105/151): filesystem-3.18-2.fc37.x86_64.rpm     21 MB/s | 1.1 MB     00:00    
(106/151): ghc-srpm-macros-1.5.0-7.fc37.noarch. 339 kB/s | 7.8 kB     00:00    
(107/151): glibc-common-2.36.9000-13.fc38.x86_6 8.0 MB/s | 304 kB     00:00    
(108/151): glibc-2.36.9000-13.fc38.x86_64.rpm    21 MB/s | 2.1 MB     00:00    
(109/151): glibc-minimal-langpack-2.36.9000-13. 954 kB/s |  25 kB     00:00    
(110/151): glibc-gconv-extra-2.36.9000-13.fc38.  16 MB/s | 1.6 MB     00:00    
(111/151): gnat-srpm-macros-4-16.fc37.noarch.rp 232 kB/s | 8.3 kB     00:00    
(112/151): go-srpm-macros-3.2.0-1.fc38.noarch.r 848 kB/s |  27 kB     00:00    
(113/151): kernel-srpm-macros-1.0-15.fc37.noarc 313 kB/s | 9.4 kB     00:00    
(114/151): libbrotli-1.0.9-9.fc37.x86_64.rpm    8.2 MB/s | 315 kB     00:00    
(115/151): libcurl-7.86.0-2.fc38.x86_64.rpm     7.5 MB/s | 305 kB     00:00    
(116/151): libffi-3.4.4-1.fc38.x86_64.rpm       846 kB/s |  38 kB     00:00    
(117/151): libdb-5.3.28-53.fc37.x86_64.rpm      9.7 MB/s | 760 kB     00:00    
(118/151): libgcc-12.2.1-3.fc38.x86_64.rpm      3.0 MB/s | 108 kB     00:00    
(119/151): libgomp-12.2.1-3.fc38.x86_64.rpm     7.0 MB/s | 295 kB     00:00    
(120/151): libssh-0.10.4-2.fc38.x86_64.rpm      4.8 MB/s | 209 kB     00:00    
(121/151): libssh-config-0.10.4-2.fc38.noarch.r 191 kB/s | 8.8 kB     00:00    
(122/151): libstdc++-12.2.1-3.fc38.x86_64.rpm    16 MB/s | 799 kB     00:00    
(123/151): libxcrypt-4.4.30-3.fc38.x86_64.rpm   2.9 MB/s | 118 kB     00:00    
(124/151): libxml2-2.10.3-2.fc38.x86_64.rpm      13 MB/s | 705 kB     00:00    
(125/151): lua-srpm-macros-1-7.fc37.noarch.rpm  173 kB/s | 8.8 kB     00:00    
(126/151): nim-srpm-macros-3-7.fc37.noarch.rpm  214 kB/s | 8.4 kB     00:00    
(127/151): ocaml-srpm-macros-7-2.fc37.noarch.rp 346 kB/s |  13 kB     00:00    
(128/151): openblas-srpm-macros-2-12.fc37.noarc 196 kB/s | 7.5 kB     00:00    
(129/151): openldap-2.6.3-1.fc38.x86_64.rpm     5.8 MB/s | 254 kB     00:00    
(130/151): p11-kit-0.24.1-3.fc37.x86_64.rpm     8.0 MB/s | 376 kB     00:00    
(131/151): p11-kit-trust-0.24.1-3.fc37.x86_64.r 3.2 MB/s | 138 kB     00:00    
(132/151): openssl-libs-3.0.5-6.fc38.x86_64.rpm  16 MB/s | 2.1 MB     00:00    
(133/151): package-notes-srpm-macros-0.5-6.fc38 242 kB/s |  11 kB     00:00    
(134/151): gdb-minimal-12.1-9.fc38.x86_64.rpm   5.1 MB/s | 3.7 MB     00:00    
(135/151): pam-1.5.2-14.fc37.x86_64.rpm          12 MB/s | 560 kB     00:00    
(136/151): pam-libs-1.5.2-14.fc37.x86_64.rpm    1.4 MB/s |  58 kB     00:00    
(137/151): perl-srpm-macros-1-46.fc37.noarch.rp 208 kB/s | 8.3 kB     00:00    
(138/151): publicsuffix-list-dafsa-20210518-5.f 1.4 MB/s |  58 kB     00:00    
(139/151): python-srpm-macros-3.11-5.fc38.noarc 562 kB/s |  24 kB     00:00    
(140/151): qt5-srpm-macros-5.15.7-1.fc38.noarch 194 kB/s | 7.9 kB     00:00    
(141/151): redhat-rpm-config-233-1.fc38.noarch. 1.9 MB/s |  81 kB     00:00    
(142/151): rpm-4.18.0-6.fc38.x86_64.rpm          12 MB/s | 572 kB     00:00    
(143/151): rpm-build-4.18.0-6.fc38.x86_64.rpm   1.7 MB/s |  77 kB     00:00    
(144/151): rpm-build-libs-4.18.0-6.fc38.x86_64. 2.0 MB/s |  94 kB     00:00    
(145/151): rpm-libs-4.18.0-6.fc38.x86_64.rpm    8.1 MB/s | 320 kB     00:00    
(146/151): rpmautospec-rpm-macros-0.3.1-1.fc38. 208 kB/s | 8.8 kB     00:00    
(147/151): rust-srpm-macros-23-1.fc38.noarch.rp 234 kB/s | 9.4 kB     00:00    
(148/151): systemd-libs-252.1-588.fc38.x86_64.r  12 MB/s | 631 kB     00:00    
(149/151): shadow-utils-4.13-1.fc38.x86_64.rpm   12 MB/s | 1.3 MB     00:00    
(150/151): which-2.21-36.fc38.x86_64.rpm        1.1 MB/s |  41 kB     00:00    
(151/151): tar-1.34-5.fc38.x86_64.rpm           6.8 MB/s | 885 kB     00:00    
--------------------------------------------------------------------------------
Total                                            25 MB/s |  51 MB     00:02     
fedora                                          1.6 MB/s | 1.6 kB     00:00    
Importing GPG key 0xEB10B464:
 Userid     : "Fedora (38) <fedora-38-primary@fedoraproject.org>"
 Fingerprint: 6A51 BBAB BA3D 5467 B617 1221 809A 8D7C EB10 B464
 From       : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary
Key imported successfully
fedora                                          1.6 MB/s | 1.6 kB     00:00    
GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary (0xEB10B464) is already installed
fedora                                          1.6 MB/s | 1.6 kB     00:00    
Importing GPG key 0x5323552A:
 Userid     : "Fedora (37) <fedora-37-primary@fedoraproject.org>"
 Fingerprint: ACB5 EE4E 831C 74BB 7C16 8D27 F55A D3FB 5323 552A
 From       : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-37-primary
Key imported successfully
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Running scriptlet: filesystem-3.18-2.fc37.x86_64                          1/1 
  Preparing        :                                                        1/1 
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  Installing       : rust-srpm-macros-23-1.fc38.noarch                    4/151 
  Installing       : qt5-srpm-macros-5.15.7-1.fc38.noarch                 5/151 
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  Installing       : perl-srpm-macros-1-46.fc37.noarch                    7/151 
  Installing       : package-notes-srpm-macros-0.5-6.fc38.noarch          8/151 
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  Installing       : nim-srpm-macros-3-7.fc37.noarch                     11/151 
  Installing       : libssh-config-0.10.4-2.fc38.noarch                  12/151 
  Installing       : kernel-srpm-macros-1.0-15.fc37.noarch               13/151 
  Installing       : gnat-srpm-macros-4-16.fc37.noarch                   14/151 
  Installing       : ghc-srpm-macros-1.5.0-7.fc37.noarch                 15/151 
  Installing       : fpc-srpm-macros-1.3-6.fc37.noarch                   16/151 
  Installing       : fedora-gpg-keys-38-0.3.noarch                       17/151 
  Installing       : fedora-release-38-0.4.noarch                        18/151 
  Installing       : fedora-release-common-38-0.4.noarch                 19/151 
  Installing       : fedora-repos-rawhide-38-0.3.noarch                  20/151 
  Installing       : fedora-repos-38-0.3.noarch                          21/151 
  Installing       : setup-2.14.2-1.fc38.noarch                          22/151 
warning: /etc/hosts created as /etc/hosts.rpmnew

  Running scriptlet: setup-2.14.2-1.fc38.noarch                          22/151 
  Installing       : filesystem-3.18-2.fc37.x86_64                       23/151 
  Installing       : basesystem-11-14.fc37.noarch                        24/151 
  Installing       : ansible-srpm-macros-1-8.1.fc38.noarch               25/151 
  Installing       : tzdata-2022f-1.fc38.noarch                          26/151 
  Installing       : pkgconf-m4-1.8.0-3.fc38.noarch                      27/151 
  Installing       : pcre2-syntax-10.40-1.fc38.1.noarch                  28/151 
  Installing       : ncurses-base-6.3-3.20220501.fc38.noarch             29/151 
  Installing       : ncurses-libs-6.3-3.20220501.fc38.x86_64             30/151 
  Installing       : glibc-gconv-extra-2.36.9000-13.fc38.x86_64          31/151 
  Running scriptlet: glibc-gconv-extra-2.36.9000-13.fc38.x86_64          31/151 
  Running scriptlet: glibc-2.36.9000-13.fc38.x86_64                      32/151 
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  Installing       : bash-5.2.2-2.fc38.x86_64                            33/151 
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  Installing       : glibc-common-2.36.9000-13.fc38.x86_64               34/151 
  Installing       : glibc-minimal-langpack-2.36.9000-13.fc38.x86_64     35/151 
  Installing       : zlib-1.2.12-5.fc38.x86_64                           36/151 
  Installing       : xz-libs-5.2.7-1.fc38.x86_64                         37/151 
  Installing       : bzip2-libs-1.0.8-12.fc38.x86_64                     38/151 
  Installing       : elfutils-libelf-0.188-3.fc38.x86_64                 39/151 
  Installing       : libuuid-2.38.1-2.fc38.x86_64                        40/151 
  Installing       : libzstd-1.5.2-3.fc38.x86_64                         41/151 
  Installing       : popt-1.19-1.fc38.x86_64                             42/151 
  Installing       : libstdc++-12.2.1-3.fc38.x86_64                      43/151 
  Installing       : libblkid-2.38.1-2.fc38.x86_64                       44/151 
  Installing       : gmp-1:6.2.1-3.fc38.x86_64                           45/151 
  Installing       : libattr-2.5.1-5.fc38.x86_64                         46/151 
  Installing       : libacl-2.3.1-4.fc38.x86_64                          47/151 
  Installing       : libcap-2.48-5.fc38.x86_64                           48/151 
  Installing       : readline-8.2-2.fc38.x86_64                          49/151 
  Installing       : libxcrypt-4.4.30-3.fc38.x86_64                      50/151 
  Installing       : lz4-libs-1.9.3-5.fc38.x86_64                        51/151 
  Installing       : systemd-libs-252.1-588.fc38.x86_64                  52/151 
  Installing       : mpfr-4.1.0-10.fc38.x86_64                           53/151 
  Installing       : dwz-0.15-1.fc38.x86_64                              54/151 
  Installing       : unzip-6.0-58.fc38.x86_64                            55/151 
  Installing       : file-libs-5.42-4.fc38.x86_64                        56/151 
  Installing       : file-5.42-4.fc38.x86_64                             57/151 
  Installing       : sqlite-libs-3.39.4-1.fc38.x86_64                    58/151 
  Installing       : alternatives-1.21-1.fc38.x86_64                     59/151 
  Installing       : libcap-ng-0.8.3-3.fc38.x86_64                       60/151 
  Installing       : audit-libs-3.0.9-1.fc38.x86_64                      61/151 
  Installing       : libcom_err-1.46.5-3.fc38.x86_64                     62/151 
  Installing       : libeconf-0.4.0-4.fc38.x86_64                        63/151 
  Installing       : pam-libs-1.5.2-14.fc37.x86_64                       64/151 
  Installing       : libsepol-3.4-3.fc38.x86_64                          65/151 
  Installing       : libsmartcols-2.38.1-2.fc38.x86_64                   66/151 
  Installing       : libunistring-1.0-2.fc38.x86_64                      67/151 
  Installing       : libidn2-2.3.4-1.fc38.x86_64                         68/151 
  Installing       : lua-libs-5.4.4-6.fc38.x86_64                        69/151 
  Installing       : pcre2-10.40-1.fc38.1.x86_64                         70/151 
  Installing       : libselinux-3.4-5.fc38.x86_64                        71/151 
  Installing       : sed-4.8-11.fc38.x86_64                              72/151 
  Installing       : grep-3.8-1.fc38.x86_64                              73/151 
  Installing       : findutils-1:4.9.0-2.fc38.x86_64                     74/151 
  Installing       : xz-5.2.7-1.fc38.x86_64                              75/151 
  Installing       : libmount-2.38.1-2.fc38.x86_64                       76/151 
  Installing       : util-linux-core-2.38.1-2.fc38.x86_64                77/151 
  Installing       : libsemanage-3.4-5.fc38.x86_64                       78/151 
  Installing       : shadow-utils-2:4.13-1.fc38.x86_64                   79/151 
  Running scriptlet: libutempter-1.2.1-7.fc38.x86_64                     80/151 
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  Installing       : zip-3.0-33.fc38.x86_64                              83/151 
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  Installing       : libfdisk-2.38.1-2.fc38.x86_64                       85/151 
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  Installing       : ed-1.18-2.fc38.x86_64                               88/151 
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  Installing       : cpio-2.13-13.fc38.x86_64                            91/151 
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  Installing       : cyrus-sasl-lib-2.1.28-8.fc38.x86_64                 93/151 
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  Installing       : p11-kit-0.24.1-3.fc37.x86_64                       109/151 
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  Installing       : libgomp-12.2.1-3.fc38.x86_64                       111/151 
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  Installing       : openssl-libs-1:3.0.5-6.fc38.x86_64                 113/151 
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  Installing       : krb5-libs-1.19.2-11.fc38.1.x86_64                  116/151 
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  Installing       : libtirpc-1.3.3-0.fc38.x86_64                       118/151 
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  Installing       : authselect-1.4.0-3.fc37.x86_64                     121/151 
  Installing       : cracklib-2.9.7-30.fc38.x86_64                      122/151 
  Installing       : libpwquality-1.4.4-11.fc38.x86_64                  123/151 
  Installing       : libnsl2-2.0.0-4.fc38.x86_64                        124/151 
  Installing       : pam-1.5.2-14.fc37.x86_64                           125/151 
  Installing       : libssh-0.10.4-2.fc38.x86_64                        126/151 
  Installing       : libarchive-3.6.1-2.fc38.x86_64                     127/151 
  Installing       : libevent-2.1.12-7.fc38.x86_64                      128/151 
  Installing       : openldap-2.6.3-1.fc38.x86_64                       129/151 
  Installing       : libcurl-7.86.0-2.fc38.x86_64                       130/151 
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  Installing       : elfutils-debuginfod-client-0.188-3.fc38.x86_64     132/151 
  Installing       : binutils-gold-2.39-5.fc38.x86_64                   133/151 
  Installing       : binutils-2.39-5.fc38.x86_64                        134/151 
  Running scriptlet: binutils-2.39-5.fc38.x86_64                        134/151 
  Installing       : elfutils-0.188-3.fc38.x86_64                       135/151 
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  Installing       : debugedit-5.0-5.fc38.x86_64                        137/151 
  Installing       : rpm-build-libs-4.18.0-6.fc38.x86_64                138/151 
  Installing       : curl-7.86.0-2.fc38.x86_64                          139/151 
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  Installing       : lua-srpm-macros-1-7.fc37.noarch                    142/151 
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  Installing       : fonts-srpm-macros-1:2.0.5-9.fc38.noarch            144/151 
  Installing       : go-srpm-macros-3.2.0-1.fc38.noarch                 145/151 
  Installing       : python-srpm-macros-3.11-5.fc38.noarch              146/151 
  Installing       : redhat-rpm-config-233-1.fc38.noarch                147/151 
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  Installing       : which-2.21-36.fc38.x86_64                          150/151 
  Installing       : info-6.8-4.fc38.x86_64                             151/151 
  Running scriptlet: filesystem-3.18-2.fc37.x86_64                      151/151 
  Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch            151/151 
  Running scriptlet: authselect-libs-1.4.0-3.fc37.x86_64                151/151 
  Running scriptlet: rpm-4.18.0-6.fc38.x86_64                           151/151 
  Running scriptlet: info-6.8-4.fc38.x86_64                             151/151 
  Verifying        : alternatives-1.21-1.fc38.x86_64                      1/151 
  Verifying        : audit-libs-3.0.9-1.fc38.x86_64                       2/151 
  Verifying        : bash-5.2.2-2.fc38.x86_64                             3/151 
  Verifying        : bzip2-1.0.8-12.fc38.x86_64                           4/151 
  Verifying        : bzip2-libs-1.0.8-12.fc38.x86_64                      5/151 
  Verifying        : coreutils-9.1-8.fc38.x86_64                          6/151 
  Verifying        : coreutils-common-9.1-8.fc38.x86_64                   7/151 
  Verifying        : cpio-2.13-13.fc38.x86_64                             8/151 
  Verifying        : cracklib-2.9.7-30.fc38.x86_64                        9/151 
  Verifying        : cyrus-sasl-lib-2.1.28-8.fc38.x86_64                 10/151 
  Verifying        : debugedit-5.0-5.fc38.x86_64                         11/151 
  Verifying        : ed-1.18-2.fc38.x86_64                               12/151 
  Verifying        : efi-srpm-macros-5-6.fc38.noarch                     13/151 
  Verifying        : file-5.42-4.fc38.x86_64                             14/151 
  Verifying        : file-libs-5.42-4.fc38.x86_64                        15/151 
  Verifying        : findutils-1:4.9.0-2.fc38.x86_64                     16/151 
  Verifying        : gawk-5.1.1-4.fc38.x86_64                            17/151 
  Verifying        : gdbm-libs-1:1.23-2.fc38.x86_64                      18/151 
  Verifying        : gmp-1:6.2.1-3.fc38.x86_64                           19/151 
  Verifying        : grep-3.8-1.fc38.x86_64                              20/151 
  Verifying        : gzip-1.12-2.fc38.x86_64                             21/151 
  Verifying        : info-6.8-4.fc38.x86_64                              22/151 
  Verifying        : jansson-2.13.1-5.fc38.x86_64                        23/151 
  Verifying        : keyutils-libs-1.6.1-5.fc38.x86_64                   24/151 
  Verifying        : krb5-libs-1.19.2-11.fc38.1.x86_64                   25/151 
  Verifying        : libacl-2.3.1-4.fc38.x86_64                          26/151 
  Verifying        : libarchive-3.6.1-2.fc38.x86_64                      27/151 
  Verifying        : libattr-2.5.1-5.fc38.x86_64                         28/151 
  Verifying        : libblkid-2.38.1-2.fc38.x86_64                       29/151 
  Verifying        : libcap-2.48-5.fc38.x86_64                           30/151 
  Verifying        : libcap-ng-0.8.3-3.fc38.x86_64                       31/151 
  Verifying        : libcom_err-1.46.5-3.fc38.x86_64                     32/151 
  Verifying        : libeconf-0.4.0-4.fc38.x86_64                        33/151 
  Verifying        : libevent-2.1.12-7.fc38.x86_64                       34/151 
  Verifying        : libfdisk-2.38.1-2.fc38.x86_64                       35/151 
  Verifying        : libidn2-2.3.4-1.fc38.x86_64                         36/151 
  Verifying        : libmount-2.38.1-2.fc38.x86_64                       37/151 
  Verifying        : libnghttp2-1.50.0-1.fc38.x86_64                     38/151 
  Verifying        : libnsl2-2.0.0-4.fc38.x86_64                         39/151 
  Verifying        : libpkgconf-1.8.0-3.fc38.x86_64                      40/151 
  Verifying        : libpsl-0.21.1-6.fc38.x86_64                         41/151 
  Verifying        : libpwquality-1.4.4-11.fc38.x86_64                   42/151 
  Verifying        : libselinux-3.4-5.fc38.x86_64                        43/151 
  Verifying        : libsemanage-3.4-5.fc38.x86_64                       44/151 
  Verifying        : libsepol-3.4-3.fc38.x86_64                          45/151 
  Verifying        : libsigsegv-2.14-3.fc38.x86_64                       46/151 
  Verifying        : libsmartcols-2.38.1-2.fc38.x86_64                   47/151 
  Verifying        : libtasn1-4.18.0-3.fc38.x86_64                       48/151 
  Verifying        : libtirpc-1.3.3-0.fc38.x86_64                        49/151 
  Verifying        : libunistring-1.0-2.fc38.x86_64                      50/151 
  Verifying        : libutempter-1.2.1-7.fc38.x86_64                     51/151 
  Verifying        : libuuid-2.38.1-2.fc38.x86_64                        52/151 
  Verifying        : libverto-0.3.2-4.fc38.x86_64                        53/151 
  Verifying        : libzstd-1.5.2-3.fc38.x86_64                         54/151 
  Verifying        : lua-libs-5.4.4-6.fc38.x86_64                        55/151 
  Verifying        : lz4-libs-1.9.3-5.fc38.x86_64                        56/151 
  Verifying        : mpfr-4.1.0-10.fc38.x86_64                           57/151 
  Verifying        : ncurses-base-6.3-3.20220501.fc38.noarch             58/151 
  Verifying        : ncurses-libs-6.3-3.20220501.fc38.x86_64             59/151 
  Verifying        : patch-2.7.6-17.fc38.x86_64                          60/151 
  Verifying        : pcre2-10.40-1.fc38.1.x86_64                         61/151 
  Verifying        : pcre2-syntax-10.40-1.fc38.1.noarch                  62/151 
  Verifying        : pkgconf-1.8.0-3.fc38.x86_64                         63/151 
  Verifying        : pkgconf-m4-1.8.0-3.fc38.noarch                      64/151 
  Verifying        : pkgconf-pkg-config-1.8.0-3.fc38.x86_64              65/151 
  Verifying        : popt-1.19-1.fc38.x86_64                             66/151 
  Verifying        : readline-8.2-2.fc38.x86_64                          67/151 
  Verifying        : sed-4.8-11.fc38.x86_64                              68/151 
  Verifying        : setup-2.14.2-1.fc38.noarch                          69/151 
  Verifying        : sqlite-libs-3.39.4-1.fc38.x86_64                    70/151 
  Verifying        : tzdata-2022f-1.fc38.noarch                          71/151 
  Verifying        : unzip-6.0-58.fc38.x86_64                            72/151 
  Verifying        : util-linux-2.38.1-2.fc38.x86_64                     73/151 
  Verifying        : util-linux-core-2.38.1-2.fc38.x86_64                74/151 
  Verifying        : xxhash-libs-0.8.1-3.fc38.x86_64                     75/151 
  Verifying        : xz-5.2.7-1.fc38.x86_64                              76/151 
  Verifying        : xz-libs-5.2.7-1.fc38.x86_64                         77/151 
  Verifying        : zip-3.0-33.fc38.x86_64                              78/151 
  Verifying        : zlib-1.2.12-5.fc38.x86_64                           79/151 
  Verifying        : zstd-1.5.2-3.fc38.x86_64                            80/151 
  Verifying        : ansible-srpm-macros-1-8.1.fc38.noarch               81/151 
  Verifying        : authselect-1.4.0-3.fc37.x86_64                      82/151 
  Verifying        : authselect-libs-1.4.0-3.fc37.x86_64                 83/151 
  Verifying        : basesystem-11-14.fc37.noarch                        84/151 
  Verifying        : binutils-2.39-5.fc38.x86_64                         85/151 
  Verifying        : binutils-gold-2.39-5.fc38.x86_64                    86/151 
  Verifying        : ca-certificates-2022.2.54-5.fc37.noarch             87/151 
  Verifying        : crypto-policies-20221110-1.git87a75f4.fc38.noarc    88/151 
  Verifying        : curl-7.86.0-2.fc38.x86_64                           89/151 
  Verifying        : diffutils-3.8-3.fc37.x86_64                         90/151 
  Verifying        : dwz-0.15-1.fc38.x86_64                              91/151 
  Verifying        : elfutils-0.188-3.fc38.x86_64                        92/151 
  Verifying        : elfutils-debuginfod-client-0.188-3.fc38.x86_64      93/151 
  Verifying        : elfutils-default-yama-scope-0.188-3.fc38.noarch     94/151 
  Verifying        : elfutils-libelf-0.188-3.fc38.x86_64                 95/151 
  Verifying        : elfutils-libs-0.188-3.fc38.x86_64                   96/151 
  Verifying        : fedora-gpg-keys-38-0.3.noarch                       97/151 
  Verifying        : fedora-release-38-0.4.noarch                        98/151 
  Verifying        : fedora-release-common-38-0.4.noarch                 99/151 
  Verifying        : fedora-release-identity-basic-38-0.4.noarch        100/151 
  Verifying        : fedora-repos-38-0.3.noarch                         101/151 
  Verifying        : fedora-repos-rawhide-38-0.3.noarch                 102/151 
  Verifying        : filesystem-3.18-2.fc37.x86_64                      103/151 
  Verifying        : fonts-srpm-macros-1:2.0.5-9.fc38.noarch            104/151 
  Verifying        : fpc-srpm-macros-1.3-6.fc37.noarch                  105/151 
  Verifying        : gdb-minimal-12.1-9.fc38.x86_64                     106/151 
  Verifying        : ghc-srpm-macros-1.5.0-7.fc37.noarch                107/151 
  Verifying        : glibc-2.36.9000-13.fc38.x86_64                     108/151 
  Verifying        : glibc-common-2.36.9000-13.fc38.x86_64              109/151 
  Verifying        : glibc-gconv-extra-2.36.9000-13.fc38.x86_64         110/151 
  Verifying        : glibc-minimal-langpack-2.36.9000-13.fc38.x86_64    111/151 
  Verifying        : gnat-srpm-macros-4-16.fc37.noarch                  112/151 
  Verifying        : go-srpm-macros-3.2.0-1.fc38.noarch                 113/151 
  Verifying        : kernel-srpm-macros-1.0-15.fc37.noarch              114/151 
  Verifying        : libbrotli-1.0.9-9.fc37.x86_64                      115/151 
  Verifying        : libcurl-7.86.0-2.fc38.x86_64                       116/151 
  Verifying        : libdb-5.3.28-53.fc37.x86_64                        117/151 
  Verifying        : libffi-3.4.4-1.fc38.x86_64                         118/151 
  Verifying        : libgcc-12.2.1-3.fc38.x86_64                        119/151 
  Verifying        : libgomp-12.2.1-3.fc38.x86_64                       120/151 
  Verifying        : libssh-0.10.4-2.fc38.x86_64                        121/151 
  Verifying        : libssh-config-0.10.4-2.fc38.noarch                 122/151 
  Verifying        : libstdc++-12.2.1-3.fc38.x86_64                     123/151 
  Verifying        : libxcrypt-4.4.30-3.fc38.x86_64                     124/151 
  Verifying        : libxml2-2.10.3-2.fc38.x86_64                       125/151 
  Verifying        : lua-srpm-macros-1-7.fc37.noarch                    126/151 
  Verifying        : nim-srpm-macros-3-7.fc37.noarch                    127/151 
  Verifying        : ocaml-srpm-macros-7-2.fc37.noarch                  128/151 
  Verifying        : openblas-srpm-macros-2-12.fc37.noarch              129/151 
  Verifying        : openldap-2.6.3-1.fc38.x86_64                       130/151 
  Verifying        : openssl-libs-1:3.0.5-6.fc38.x86_64                 131/151 
  Verifying        : p11-kit-0.24.1-3.fc37.x86_64                       132/151 
  Verifying        : p11-kit-trust-0.24.1-3.fc37.x86_64                 133/151 
  Verifying        : package-notes-srpm-macros-0.5-6.fc38.noarch        134/151 
  Verifying        : pam-1.5.2-14.fc37.x86_64                           135/151 
  Verifying        : pam-libs-1.5.2-14.fc37.x86_64                      136/151 
  Verifying        : perl-srpm-macros-1-46.fc37.noarch                  137/151 
  Verifying        : publicsuffix-list-dafsa-20210518-5.fc37.noarch     138/151 
  Verifying        : python-srpm-macros-3.11-5.fc38.noarch              139/151 
  Verifying        : qt5-srpm-macros-5.15.7-1.fc38.noarch               140/151 
  Verifying        : redhat-rpm-config-233-1.fc38.noarch                141/151 
  Verifying        : rpm-4.18.0-6.fc38.x86_64                           142/151 
  Verifying        : rpm-build-4.18.0-6.fc38.x86_64                     143/151 
  Verifying        : rpm-build-libs-4.18.0-6.fc38.x86_64                144/151 
  Verifying        : rpm-libs-4.18.0-6.fc38.x86_64                      145/151 
  Verifying        : rpmautospec-rpm-macros-0.3.1-1.fc38.noarch         146/151 
  Verifying        : rust-srpm-macros-23-1.fc38.noarch                  147/151 
  Verifying        : shadow-utils-2:4.13-1.fc38.x86_64                  148/151 
  Verifying        : systemd-libs-252.1-588.fc38.x86_64                 149/151 
  Verifying        : tar-2:1.34-5.fc38.x86_64                           150/151 
  Verifying        : which-2.21-36.fc38.x86_64                          151/151 

Installed:
  alternatives-1.21-1.fc38.x86_64                                               
  ansible-srpm-macros-1-8.1.fc38.noarch                                         
  audit-libs-3.0.9-1.fc38.x86_64                                                
  authselect-1.4.0-3.fc37.x86_64                                                
  authselect-libs-1.4.0-3.fc37.x86_64                                           
  basesystem-11-14.fc37.noarch                                                  
  bash-5.2.2-2.fc38.x86_64                                                      
  binutils-2.39-5.fc38.x86_64                                                   
  binutils-gold-2.39-5.fc38.x86_64                                              
  bzip2-1.0.8-12.fc38.x86_64                                                    
  bzip2-libs-1.0.8-12.fc38.x86_64                                               
  ca-certificates-2022.2.54-5.fc37.noarch                                       
  coreutils-9.1-8.fc38.x86_64                                                   
  coreutils-common-9.1-8.fc38.x86_64                                            
  cpio-2.13-13.fc38.x86_64                                                      
  cracklib-2.9.7-30.fc38.x86_64                                                 
  crypto-policies-20221110-1.git87a75f4.fc38.noarch                             
  curl-7.86.0-2.fc38.x86_64                                                     
  cyrus-sasl-lib-2.1.28-8.fc38.x86_64                                           
  debugedit-5.0-5.fc38.x86_64                                                   
  diffutils-3.8-3.fc37.x86_64                                                   
  dwz-0.15-1.fc38.x86_64                                                        
  ed-1.18-2.fc38.x86_64                                                         
  efi-srpm-macros-5-6.fc38.noarch                                               
  elfutils-0.188-3.fc38.x86_64                                                  
  elfutils-debuginfod-client-0.188-3.fc38.x86_64                                
  elfutils-default-yama-scope-0.188-3.fc38.noarch                               
  elfutils-libelf-0.188-3.fc38.x86_64                                           
  elfutils-libs-0.188-3.fc38.x86_64                                             
  fedora-gpg-keys-38-0.3.noarch                                                 
  fedora-release-38-0.4.noarch                                                  
  fedora-release-common-38-0.4.noarch                                           
  fedora-release-identity-basic-38-0.4.noarch                                   
  fedora-repos-38-0.3.noarch                                                    
  fedora-repos-rawhide-38-0.3.noarch                                            
  file-5.42-4.fc38.x86_64                                                       
  file-libs-5.42-4.fc38.x86_64                                                  
  filesystem-3.18-2.fc37.x86_64                                                 
  findutils-1:4.9.0-2.fc38.x86_64                                               
  fonts-srpm-macros-1:2.0.5-9.fc38.noarch                                       
  fpc-srpm-macros-1.3-6.fc37.noarch                                             
  gawk-5.1.1-4.fc38.x86_64                                                      
  gdb-minimal-12.1-9.fc38.x86_64                                                
  gdbm-libs-1:1.23-2.fc38.x86_64                                                
  ghc-srpm-macros-1.5.0-7.fc37.noarch                                           
  glibc-2.36.9000-13.fc38.x86_64                                                
  glibc-common-2.36.9000-13.fc38.x86_64                                         
  glibc-gconv-extra-2.36.9000-13.fc38.x86_64                                    
  glibc-minimal-langpack-2.36.9000-13.fc38.x86_64                               
  gmp-1:6.2.1-3.fc38.x86_64                                                     
  gnat-srpm-macros-4-16.fc37.noarch                                             
  go-srpm-macros-3.2.0-1.fc38.noarch                                            
  grep-3.8-1.fc38.x86_64                                                        
  gzip-1.12-2.fc38.x86_64                                                       
  info-6.8-4.fc38.x86_64                                                        
  jansson-2.13.1-5.fc38.x86_64                                                  
  kernel-srpm-macros-1.0-15.fc37.noarch                                         
  keyutils-libs-1.6.1-5.fc38.x86_64                                             
  krb5-libs-1.19.2-11.fc38.1.x86_64                                             
  libacl-2.3.1-4.fc38.x86_64                                                    
  libarchive-3.6.1-2.fc38.x86_64                                                
  libattr-2.5.1-5.fc38.x86_64                                                   
  libblkid-2.38.1-2.fc38.x86_64                                                 
  libbrotli-1.0.9-9.fc37.x86_64                                                 
  libcap-2.48-5.fc38.x86_64                                                     
  libcap-ng-0.8.3-3.fc38.x86_64                                                 
  libcom_err-1.46.5-3.fc38.x86_64                                               
  libcurl-7.86.0-2.fc38.x86_64                                                  
  libdb-5.3.28-53.fc37.x86_64                                                   
  libeconf-0.4.0-4.fc38.x86_64                                                  
  libevent-2.1.12-7.fc38.x86_64                                                 
  libfdisk-2.38.1-2.fc38.x86_64                                                 
  libffi-3.4.4-1.fc38.x86_64                                                    
  libgcc-12.2.1-3.fc38.x86_64                                                   
  libgomp-12.2.1-3.fc38.x86_64                                                  
  libidn2-2.3.4-1.fc38.x86_64                                                   
  libmount-2.38.1-2.fc38.x86_64                                                 
  libnghttp2-1.50.0-1.fc38.x86_64                                               
  libnsl2-2.0.0-4.fc38.x86_64                                                   
  libpkgconf-1.8.0-3.fc38.x86_64                                                
  libpsl-0.21.1-6.fc38.x86_64                                                   
  libpwquality-1.4.4-11.fc38.x86_64                                             
  libselinux-3.4-5.fc38.x86_64                                                  
  libsemanage-3.4-5.fc38.x86_64                                                 
  libsepol-3.4-3.fc38.x86_64                                                    
  libsigsegv-2.14-3.fc38.x86_64                                                 
  libsmartcols-2.38.1-2.fc38.x86_64                                             
  libssh-0.10.4-2.fc38.x86_64                                                   
  libssh-config-0.10.4-2.fc38.noarch                                            
  libstdc++-12.2.1-3.fc38.x86_64                                                
  libtasn1-4.18.0-3.fc38.x86_64                                                 
  libtirpc-1.3.3-0.fc38.x86_64                                                  
  libunistring-1.0-2.fc38.x86_64                                                
  libutempter-1.2.1-7.fc38.x86_64                                               
  libuuid-2.38.1-2.fc38.x86_64                                                  
  libverto-0.3.2-4.fc38.x86_64                                                  
  libxcrypt-4.4.30-3.fc38.x86_64                                                
  libxml2-2.10.3-2.fc38.x86_64                                                  
  libzstd-1.5.2-3.fc38.x86_64                                                   
  lua-libs-5.4.4-6.fc38.x86_64                                                  
  lua-srpm-macros-1-7.fc37.noarch                                               
  lz4-libs-1.9.3-5.fc38.x86_64                                                  
  mpfr-4.1.0-10.fc38.x86_64                                                     
  ncurses-base-6.3-3.20220501.fc38.noarch                                       
  ncurses-libs-6.3-3.20220501.fc38.x86_64                                       
  nim-srpm-macros-3-7.fc37.noarch                                               
  ocaml-srpm-macros-7-2.fc37.noarch                                             
  openblas-srpm-macros-2-12.fc37.noarch                                         
  openldap-2.6.3-1.fc38.x86_64                                                  
  openssl-libs-1:3.0.5-6.fc38.x86_64                                            
  p11-kit-0.24.1-3.fc37.x86_64                                                  
  p11-kit-trust-0.24.1-3.fc37.x86_64                                            
  package-notes-srpm-macros-0.5-6.fc38.noarch                                   
  pam-1.5.2-14.fc37.x86_64                                                      
  pam-libs-1.5.2-14.fc37.x86_64                                                 
  patch-2.7.6-17.fc38.x86_64                                                    
  pcre2-10.40-1.fc38.1.x86_64                                                   
  pcre2-syntax-10.40-1.fc38.1.noarch                                            
  perl-srpm-macros-1-46.fc37.noarch                                             
  pkgconf-1.8.0-3.fc38.x86_64                                                   
  pkgconf-m4-1.8.0-3.fc38.noarch                                                
  pkgconf-pkg-config-1.8.0-3.fc38.x86_64                                        
  popt-1.19-1.fc38.x86_64                                                       
  publicsuffix-list-dafsa-20210518-5.fc37.noarch                                
  python-srpm-macros-3.11-5.fc38.noarch                                         
  qt5-srpm-macros-5.15.7-1.fc38.noarch                                          
  readline-8.2-2.fc38.x86_64                                                    
  redhat-rpm-config-233-1.fc38.noarch                                           
  rpm-4.18.0-6.fc38.x86_64                                                      
  rpm-build-4.18.0-6.fc38.x86_64                                                
  rpm-build-libs-4.18.0-6.fc38.x86_64                                           
  rpm-libs-4.18.0-6.fc38.x86_64                                                 
  rpmautospec-rpm-macros-0.3.1-1.fc38.noarch                                    
  rust-srpm-macros-23-1.fc38.noarch                                             
  sed-4.8-11.fc38.x86_64                                                        
  setup-2.14.2-1.fc38.noarch                                                    
  shadow-utils-2:4.13-1.fc38.x86_64                                             
  sqlite-libs-3.39.4-1.fc38.x86_64                                              
  systemd-libs-252.1-588.fc38.x86_64                                            
  tar-2:1.34-5.fc38.x86_64                                                      
  tzdata-2022f-1.fc38.noarch                                                    
  unzip-6.0-58.fc38.x86_64                                                      
  util-linux-2.38.1-2.fc38.x86_64                                               
  util-linux-core-2.38.1-2.fc38.x86_64                                          
  which-2.21-36.fc38.x86_64                                                     
  xxhash-libs-0.8.1-3.fc38.x86_64                                               
  xz-5.2.7-1.fc38.x86_64                                                        
  xz-libs-5.2.7-1.fc38.x86_64                                                   
  zip-3.0-33.fc38.x86_64                                                        
  zlib-1.2.12-5.fc38.x86_64                                                     
  zstd-1.5.2-3.fc38.x86_64                                                      

Complete!
Finish: dnf install
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: lz4-libs-1.9.3-5.fc38.x86_64
coreutils-9.1-8.fc38.x86_64
rpmautospec-rpm-macros-0.3.1-1.fc38.noarch
cyrus-sasl-lib-2.1.28-8.fc38.x86_64
pkgconf-1.8.0-3.fc38.x86_64
elfutils-0.188-3.fc38.x86_64
rpm-build-4.18.0-6.fc38.x86_64
grep-3.8-1.fc38.x86_64
libcap-2.48-5.fc38.x86_64
libgomp-12.2.1-3.fc38.x86_64
readline-8.2-2.fc38.x86_64
perl-srpm-macros-1-46.fc37.noarch
fpc-srpm-macros-1.3-6.fc37.noarch
libselinux-3.4-5.fc38.x86_64
libpkgconf-1.8.0-3.fc38.x86_64
unzip-6.0-58.fc38.x86_64
ansible-srpm-macros-1-8.1.fc38.noarch
bzip2-libs-1.0.8-12.fc38.x86_64
audit-libs-3.0.9-1.fc38.x86_64
ocaml-srpm-macros-7-2.fc37.noarch
zip-3.0-33.fc38.x86_64
p11-kit-trust-0.24.1-3.fc37.x86_64
pam-1.5.2-14.fc37.x86_64
libcurl-7.86.0-2.fc38.x86_64
libattr-2.5.1-5.fc38.x86_64
coreutils-common-9.1-8.fc38.x86_64
libxcrypt-4.4.30-3.fc38.x86_64
libfdisk-2.38.1-2.fc38.x86_64
libsemanage-3.4-5.fc38.x86_64
filesystem-3.18-2.fc37.x86_64
gzip-1.12-2.fc38.x86_64
authselect-libs-1.4.0-3.fc37.x86_64
curl-7.86.0-2.fc38.x86_64
zlib-1.2.12-5.fc38.x86_64
rpm-libs-4.18.0-6.fc38.x86_64
package-notes-srpm-macros-0.5-6.fc38.noarch
libffi-3.4.4-1.fc38.x86_64
libverto-0.3.2-4.fc38.x86_64
sqlite-libs-3.39.4-1.fc38.x86_64
elfutils-debuginfod-client-0.188-3.fc38.x86_64
patch-2.7.6-17.fc38.x86_64
libstdc++-12.2.1-3.fc38.x86_64
libzstd-1.5.2-3.fc38.x86_64
kernel-srpm-macros-1.0-15.fc37.noarch
fedora-release-38-0.4.noarch
libtasn1-4.18.0-3.fc38.x86_64
libmount-2.38.1-2.fc38.x86_64
ncurses-base-6.3-3.20220501.fc38.noarch
xz-libs-5.2.7-1.fc38.x86_64
mpfr-4.1.0-10.fc38.x86_64
openssl-libs-3.0.5-6.fc38.x86_64
authselect-1.4.0-3.fc37.x86_64
libtirpc-1.3.3-0.fc38.x86_64
setup-2.14.2-1.fc38.noarch
xz-5.2.7-1.fc38.x86_64
libssh-0.10.4-2.fc38.x86_64
rpm-build-libs-4.18.0-6.fc38.x86_64
openblas-srpm-macros-2-12.fc37.noarch
krb5-libs-1.19.2-11.fc38.1.x86_64
fonts-srpm-macros-2.0.5-9.fc38.noarch
pkgconf-m4-1.8.0-3.fc38.noarch
rpm-4.18.0-6.fc38.x86_64
libeconf-0.4.0-4.fc38.x86_64
libblkid-2.38.1-2.fc38.x86_64
alternatives-1.21-1.fc38.x86_64
fedora-release-identity-basic-38-0.4.noarch
jansson-2.13.1-5.fc38.x86_64
libnsl2-2.0.0-4.fc38.x86_64
publicsuffix-list-dafsa-20210518-5.fc37.noarch
basesystem-11-14.fc37.noarch
libxml2-2.10.3-2.fc38.x86_64
findutils-4.9.0-2.fc38.x86_64
binutils-2.39-5.fc38.x86_64
xxhash-libs-0.8.1-3.fc38.x86_64
fedora-repos-rawhide-38-0.3.noarch
crypto-policies-20221110-1.git87a75f4.fc38.noarch
libsepol-3.4-3.fc38.x86_64
gpg-pubkey-5323552a-6112bcdc
lua-srpm-macros-1-7.fc37.noarch
glibc-minimal-langpack-2.36.9000-13.fc38.x86_64
nim-srpm-macros-3-7.fc37.noarch
ca-certificates-2022.2.54-5.fc37.noarch
elfutils-default-yama-scope-0.188-3.fc38.noarch
gmp-6.2.1-3.fc38.x86_64
popt-1.19-1.fc38.x86_64
cracklib-2.9.7-30.fc38.x86_64
pcre2-10.40-1.fc38.1.x86_64
fedora-repos-38-0.3.noarch
go-srpm-macros-3.2.0-1.fc38.noarch
which-2.21-36.fc38.x86_64
binutils-gold-2.39-5.fc38.x86_64
bash-5.2.2-2.fc38.x86_64
dwz-0.15-1.fc38.x86_64
gawk-5.1.1-4.fc38.x86_64
systemd-libs-252.1-588.fc38.x86_64
libgcc-12.2.1-3.fc38.x86_64
bzip2-1.0.8-12.fc38.x86_64
pkgconf-pkg-config-1.8.0-3.fc38.x86_64
util-linux-2.38.1-2.fc38.x86_64
libpwquality-1.4.4-11.fc38.x86_64
libssh-config-0.10.4-2.fc38.noarch
libarchive-3.6.1-2.fc38.x86_64
pam-libs-1.5.2-14.fc37.x86_64
gdbm-libs-1.23-2.fc38.x86_64
util-linux-core-2.38.1-2.fc38.x86_64
libsigsegv-2.14-3.fc38.x86_64
libunistring-1.0-2.fc38.x86_64
gdb-minimal-12.1-9.fc38.x86_64
libcom_err-1.46.5-3.fc38.x86_64
file-5.42-4.fc38.x86_64
elfutils-libelf-0.188-3.fc38.x86_64
libnghttp2-1.50.0-1.fc38.x86_64
cpio-2.13-13.fc38.x86_64
fedora-release-common-38-0.4.noarch
info-6.8-4.fc38.x86_64
libutempter-1.2.1-7.fc38.x86_64
python-srpm-macros-3.11-5.fc38.noarch
tar-1.34-5.fc38.x86_64
debugedit-5.0-5.fc38.x86_64
fedora-gpg-keys-38-0.3.noarch
libidn2-2.3.4-1.fc38.x86_64
keyutils-libs-1.6.1-5.fc38.x86_64
glibc-gconv-extra-2.36.9000-13.fc38.x86_64
diffutils-3.8-3.fc37.x86_64
libpsl-0.21.1-6.fc38.x86_64
libacl-2.3.1-4.fc38.x86_64
efi-srpm-macros-5-6.fc38.noarch
rust-srpm-macros-23-1.fc38.noarch
ncurses-libs-6.3-3.20220501.fc38.x86_64
glibc-2.36.9000-13.fc38.x86_64
openldap-2.6.3-1.fc38.x86_64
ghc-srpm-macros-1.5.0-7.fc37.noarch
libsmartcols-2.38.1-2.fc38.x86_64
elfutils-libs-0.188-3.fc38.x86_64
sed-4.8-11.fc38.x86_64
gpg-pubkey-eb10b464-6202d9c6
glibc-common-2.36.9000-13.fc38.x86_64
shadow-utils-4.13-1.fc38.x86_64
libevent-2.1.12-7.fc38.x86_64
lua-libs-5.4.4-6.fc38.x86_64
redhat-rpm-config-233-1.fc38.noarch
zstd-1.5.2-3.fc38.x86_64
qt5-srpm-macros-5.15.7-1.fc38.noarch
tzdata-2022f-1.fc38.noarch
file-libs-5.42-4.fc38.x86_64
pcre2-syntax-10.40-1.fc38.1.noarch
libdb-5.3.28-53.fc37.x86_64
libcap-ng-0.8.3-3.fc38.x86_64
libbrotli-1.0.9-9.fc37.x86_64
gnat-srpm-macros-4-16.fc37.noarch
ed-1.18-2.fc38.x86_64
libuuid-2.38.1-2.fc38.x86_64
p11-kit-0.24.1-3.fc37.x86_64
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1658448000
Wrote: /builddir/build/SRPMS/percolator-3.05-10.fc38.src.rpm
Finish: rpmbuild -bs
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-x86_64-1668321698.617486/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-x86_64-1668321698.617486/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-x86_64-1668321698.617486/root/var/log/dnf.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-_t6tuudt/percolator/percolator.spec) Config(child) 1 minutes 36 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
Finish: run
Running (timeout=108000): unbuffer mock --rebuild /var/lib/copr-rpmbuild/results/percolator-3.05-10.fc38.src.rpm --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1668321698.617486 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 3.3 starting (python version = 3.10.4, NVR = mock-3.3-1.fc35)...
Start(bootstrap): init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish(bootstrap): init plugins
Start: init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish: init plugins
INFO: Signal handler active
Start: run
INFO: Start(/var/lib/copr-rpmbuild/results/percolator-3.05-10.fc38.src.rpm)  Config(fedora-rawhide-x86_64)
Start: clean chroot
Finish: clean chroot
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1668321698.617486/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1668321698.617486/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
INFO: enabled HW Info plugin
Mock Version: 3.3
INFO: Mock Version: 3.3
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1668321698.617486/root.
INFO: calling preinit hooks
INFO: enabled root cache
Start: unpacking root cache
Finish: unpacking root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
Mock Version: 3.3
INFO: Mock Version: 3.3
Start: dnf update
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                  55 kB/s | 3.0 kB     00:00    
Copr repository                                  54 MB/s |  34 MB     00:00    
fedora                                          225 kB/s |  12 kB     00:00    
Dependencies resolved.
Nothing to do.
Complete!
Finish: dnf update
Finish: chroot init
Start: build phase for percolator-3.05-10.fc38.src.rpm
Start: build setup for percolator-3.05-10.fc38.src.rpm
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1658448000
Wrote: /builddir/build/SRPMS/percolator-3.05-10.fc38.src.rpm
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                  35 kB/s | 3.0 kB     00:00    
Copr repository                                  68 MB/s |  34 MB     00:00    
fedora                                          261 kB/s |  12 kB     00:00    
Dependencies resolved.
================================================================================
 Package                    Arch    Version                    Repository  Size
================================================================================
Installing:
 boost-devel                x86_64  1.78.0-9.fc37              fedora      13 M
 boost-static               x86_64  1.78.0-9.fc37              fedora     3.6 M
 bzip2-devel                x86_64  1.0.8-12.fc38              copr_base  214 k
 cmake                      x86_64  3.25.0-0.6.rc4.fc38        fedora     6.8 M
 gcc                        x86_64  12.2.1-3.fc38              fedora      33 M
 gcc-c++                    x86_64  12.2.1-3.fc38              fedora      13 M
 libtirpc-devel             x86_64  1.3.3-0.fc38               copr_base  113 k
 make                       x86_64  1:4.4-1.fc38               copr_base  571 k
 sqlite-devel               x86_64  3.39.4-1.fc38              copr_base  143 k
 tokyocabinet-devel         x86_64  1.4.48-20.fc38             copr_base   89 k
 xerces-c-devel             x86_64  3.2.3-7.fc38               copr_base  435 k
 xsd                        x86_64  4.1.0-0.10.a11.fc38        copr_base  1.2 M
 zlib-devel                 x86_64  1.2.12-5.fc38              copr_base   45 k
Installing dependencies:
 annobin-docs               noarch  10.92-1.fc38               fedora      92 k
 annobin-plugin-gcc         x86_64  10.92-1.fc38               fedora     888 k
 boost                      x86_64  1.78.0-9.fc37              fedora      14 k
 boost-atomic               x86_64  1.78.0-9.fc37              fedora      20 k
 boost-chrono               x86_64  1.78.0-9.fc37              fedora      27 k
 boost-container            x86_64  1.78.0-9.fc37              fedora      40 k
 boost-context              x86_64  1.78.0-9.fc37              fedora      17 k
 boost-contract             x86_64  1.78.0-9.fc37              fedora      47 k
 boost-coroutine            x86_64  1.78.0-9.fc37              fedora      22 k
 boost-date-time            x86_64  1.78.0-9.fc37              fedora      16 k
 boost-fiber                x86_64  1.78.0-9.fc37              fedora      42 k
 boost-filesystem           x86_64  1.78.0-9.fc37              fedora      66 k
 boost-graph                x86_64  1.78.0-9.fc37              fedora     149 k
 boost-iostreams            x86_64  1.78.0-9.fc37              fedora      42 k
 boost-json                 x86_64  1.78.0-9.fc37              fedora     111 k
 boost-locale               x86_64  1.78.0-9.fc37              fedora     218 k
 boost-log                  x86_64  1.78.0-9.fc37              fedora     483 k
 boost-math                 x86_64  1.78.0-9.fc37              fedora     204 k
 boost-nowide               x86_64  1.78.0-9.fc37              fedora      21 k
 boost-numpy3               x86_64  1.78.0-9.fc37              fedora      30 k
 boost-program-options      x86_64  1.78.0-9.fc37              fedora     107 k
 boost-python3              x86_64  1.78.0-9.fc37              fedora      96 k
 boost-random               x86_64  1.78.0-9.fc37              fedora      26 k
 boost-regex                x86_64  1.78.0-9.fc37              fedora     113 k
 boost-serialization        x86_64  1.78.0-9.fc37              fedora     134 k
 boost-stacktrace           x86_64  1.78.0-9.fc37              fedora      30 k
 boost-system               x86_64  1.78.0-9.fc37              fedora      16 k
 boost-test                 x86_64  1.78.0-9.fc37              fedora     234 k
 boost-thread               x86_64  1.78.0-9.fc37              fedora      59 k
 boost-timer                x86_64  1.78.0-9.fc37              fedora      26 k
 boost-type_erasure         x86_64  1.78.0-9.fc37              fedora      35 k
 boost-wave                 x86_64  1.78.0-9.fc37              fedora     204 k
 cmake-data                 noarch  3.25.0-0.6.rc4.fc38        fedora     2.2 M
 cmake-filesystem           x86_64  3.25.0-0.6.rc4.fc38        fedora      16 k
 cmake-rpm-macros           noarch  3.25.0-0.6.rc4.fc38        fedora      16 k
 cpp                        x86_64  12.2.1-3.fc38              fedora      11 M
 emacs-filesystem           noarch  1:28.1-3.fc37              fedora     9.5 k
 expat                      x86_64  2.4.8-2.fc38               copr_base  110 k
 flexiblas                  x86_64  3.2.1-2.fc38               copr_base   33 k
 flexiblas-netlib           x86_64  3.2.1-2.fc38               copr_base  3.1 M
 flexiblas-openblas-openmp  x86_64  3.2.1-2.fc38               copr_base   18 k
 gc                         x86_64  8.2.2-1.fc38               copr_base  110 k
 gcc-plugin-annobin         x86_64  12.2.1-3.fc38              fedora      53 k
 glibc-devel                x86_64  2.36.9000-13.fc38          fedora      42 k
 glibc-headers-x86          noarch  2.36.9000-13.fc38          fedora     520 k
 guile22                    x86_64  2.2.7-6.fc38               copr_base  6.4 M
 jsoncpp                    x86_64  1.9.5-3.fc37               fedora      98 k
 kernel-headers             x86_64  6.1.0-0.rc4.git0.1.fc38    fedora     1.5 M
 libb2                      x86_64  0.98.1-7.fc38              copr_base   25 k
 libcutl                    x86_64  1.10.0-25.fc38             copr_base  312 k
 libgfortran                x86_64  12.2.1-3.fc38              fedora     900 k
 libicu                     x86_64  71.1-2.fc38                copr_base   10 M
 libicu-devel               x86_64  71.1-2.fc38                copr_base  842 k
 libmpc                     x86_64  1.2.1-5.fc38               copr_base   61 k
 libquadmath                x86_64  12.2.1-3.fc38              fedora     201 k
 libquadmath-devel          x86_64  12.2.1-3.fc38              fedora      42 k
 libstdc++-devel            x86_64  12.2.1-3.fc38              fedora     2.5 M
 libtool-ltdl               x86_64  2.4.7-2.fc37               fedora      37 k
 libuv                      x86_64  1:1.44.2-2.fc38            copr_base  152 k
 libxcrypt-devel            x86_64  4.4.30-3.fc38              fedora      29 k
 mpdecimal                  x86_64  2.5.1-4.fc38               copr_base  102 k
 openblas                   x86_64  0.3.21-3.fc38              copr_base   36 k
 openblas-openmp            x86_64  0.3.21-3.fc38              copr_base  5.1 M
 python-pip-wheel           noarch  22.2.2-2.fc38              fedora     1.4 M
 python-setuptools-wheel    noarch  65.5.1-1.fc38              fedora     715 k
 python3                    x86_64  3.11.0-1.fc38              fedora      27 k
 python3-libs               x86_64  3.11.0-1.fc38              fedora     9.6 M
 python3-numpy              x86_64  1:1.23.4-1.fc38            fedora     7.6 M
 rhash                      x86_64  1.4.3-1.fc38               copr_base  194 k
 sqlite                     x86_64  3.39.4-1.fc38              copr_base  800 k
 tokyocabinet               x86_64  1.4.48-20.fc38             copr_base  506 k
 vim-filesystem             noarch  2:9.0.828-1.fc38           fedora      19 k
 xerces-c                   x86_64  3.2.3-7.fc38               copr_base  959 k

Transaction Summary
================================================================================
Install  86 Packages

Total download size: 143 M
Installed size: 654 M
Downloading Packages:
(1/86): expat-2.4.8-2.fc38.x86_64.rpm           949 kB/s | 110 kB     00:00    
(2/86): flexiblas-3.2.1-2.fc38.x86_64.rpm       285 kB/s |  33 kB     00:00    
(3/86): bzip2-devel-1.0.8-12.fc38.x86_64.rpm    1.7 MB/s | 214 kB     00:00    
(4/86): flexiblas-openblas-openmp-3.2.1-2.fc38. 986 kB/s |  18 kB     00:00    
(5/86): gc-8.2.2-1.fc38.x86_64.rpm              4.5 MB/s | 110 kB     00:00    
(6/86): flexiblas-netlib-3.2.1-2.fc38.x86_64.rp  58 MB/s | 3.1 MB     00:00    
(7/86): libb2-0.98.1-7.fc38.x86_64.rpm          521 kB/s |  25 kB     00:00    
(8/86): guile22-2.2.7-6.fc38.x86_64.rpm          64 MB/s | 6.4 MB     00:00    
(9/86): libcutl-1.10.0-25.fc38.x86_64.rpm       4.5 MB/s | 312 kB     00:00    
(10/86): libmpc-1.2.1-5.fc38.x86_64.rpm         3.1 MB/s |  61 kB     00:00    
(11/86): libicu-devel-71.1-2.fc38.x86_64.rpm     22 MB/s | 842 kB     00:00    
(12/86): libtirpc-devel-1.3.3-0.fc38.x86_64.rpm 6.3 MB/s | 113 kB     00:00    
(13/86): libuv-1.44.2-2.fc38.x86_64.rpm         8.9 MB/s | 152 kB     00:00    
(14/86): make-4.4-1.fc38.x86_64.rpm              24 MB/s | 571 kB     00:00    
(15/86): mpdecimal-2.5.1-4.fc38.x86_64.rpm      4.8 MB/s | 102 kB     00:00    
(16/86): openblas-0.3.21-3.fc38.x86_64.rpm      1.9 MB/s |  36 kB     00:00    
(17/86): rhash-1.4.3-1.fc38.x86_64.rpm          8.9 MB/s | 194 kB     00:00    
(18/86): libicu-71.1-2.fc38.x86_64.rpm           58 MB/s |  10 MB     00:00    
(19/86): openblas-openmp-0.3.21-3.fc38.x86_64.r  65 MB/s | 5.1 MB     00:00    
(20/86): sqlite-3.39.4-1.fc38.x86_64.rpm         14 MB/s | 800 kB     00:00    
(21/86): sqlite-devel-3.39.4-1.fc38.x86_64.rpm  6.0 MB/s | 143 kB     00:00    
(22/86): xerces-c-3.2.3-7.fc38.x86_64.rpm        52 MB/s | 959 kB     00:00    
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  Verifying        : libquadmath-12.2.1-3.fc38.x86_64                     76/86 
  Verifying        : libquadmath-devel-12.2.1-3.fc38.x86_64               77/86 
  Verifying        : libstdc++-devel-12.2.1-3.fc38.x86_64                 78/86 
  Verifying        : libtool-ltdl-2.4.7-2.fc37.x86_64                     79/86 
  Verifying        : libxcrypt-devel-4.4.30-3.fc38.x86_64                 80/86 
  Verifying        : python-pip-wheel-22.2.2-2.fc38.noarch                81/86 
  Verifying        : python-setuptools-wheel-65.5.1-1.fc38.noarch         82/86 
  Verifying        : python3-3.11.0-1.fc38.x86_64                         83/86 
  Verifying        : python3-libs-3.11.0-1.fc38.x86_64                    84/86 
  Verifying        : python3-numpy-1:1.23.4-1.fc38.x86_64                 85/86 
  Verifying        : vim-filesystem-2:9.0.828-1.fc38.noarch               86/86 

Installed:
  annobin-docs-10.92-1.fc38.noarch                                              
  annobin-plugin-gcc-10.92-1.fc38.x86_64                                        
  boost-1.78.0-9.fc37.x86_64                                                    
  boost-atomic-1.78.0-9.fc37.x86_64                                             
  boost-chrono-1.78.0-9.fc37.x86_64                                             
  boost-container-1.78.0-9.fc37.x86_64                                          
  boost-context-1.78.0-9.fc37.x86_64                                            
  boost-contract-1.78.0-9.fc37.x86_64                                           
  boost-coroutine-1.78.0-9.fc37.x86_64                                          
  boost-date-time-1.78.0-9.fc37.x86_64                                          
  boost-devel-1.78.0-9.fc37.x86_64                                              
  boost-fiber-1.78.0-9.fc37.x86_64                                              
  boost-filesystem-1.78.0-9.fc37.x86_64                                         
  boost-graph-1.78.0-9.fc37.x86_64                                              
  boost-iostreams-1.78.0-9.fc37.x86_64                                          
  boost-json-1.78.0-9.fc37.x86_64                                               
  boost-locale-1.78.0-9.fc37.x86_64                                             
  boost-log-1.78.0-9.fc37.x86_64                                                
  boost-math-1.78.0-9.fc37.x86_64                                               
  boost-nowide-1.78.0-9.fc37.x86_64                                             
  boost-numpy3-1.78.0-9.fc37.x86_64                                             
  boost-program-options-1.78.0-9.fc37.x86_64                                    
  boost-python3-1.78.0-9.fc37.x86_64                                            
  boost-random-1.78.0-9.fc37.x86_64                                             
  boost-regex-1.78.0-9.fc37.x86_64                                              
  boost-serialization-1.78.0-9.fc37.x86_64                                      
  boost-stacktrace-1.78.0-9.fc37.x86_64                                         
  boost-static-1.78.0-9.fc37.x86_64                                             
  boost-system-1.78.0-9.fc37.x86_64                                             
  boost-test-1.78.0-9.fc37.x86_64                                               
  boost-thread-1.78.0-9.fc37.x86_64                                             
  boost-timer-1.78.0-9.fc37.x86_64                                              
  boost-type_erasure-1.78.0-9.fc37.x86_64                                       
  boost-wave-1.78.0-9.fc37.x86_64                                               
  bzip2-devel-1.0.8-12.fc38.x86_64                                              
  cmake-3.25.0-0.6.rc4.fc38.x86_64                                              
  cmake-data-3.25.0-0.6.rc4.fc38.noarch                                         
  cmake-filesystem-3.25.0-0.6.rc4.fc38.x86_64                                   
  cmake-rpm-macros-3.25.0-0.6.rc4.fc38.noarch                                   
  cpp-12.2.1-3.fc38.x86_64                                                      
  emacs-filesystem-1:28.1-3.fc37.noarch                                         
  expat-2.4.8-2.fc38.x86_64                                                     
  flexiblas-3.2.1-2.fc38.x86_64                                                 
  flexiblas-netlib-3.2.1-2.fc38.x86_64                                          
  flexiblas-openblas-openmp-3.2.1-2.fc38.x86_64                                 
  gc-8.2.2-1.fc38.x86_64                                                        
  gcc-12.2.1-3.fc38.x86_64                                                      
  gcc-c++-12.2.1-3.fc38.x86_64                                                  
  gcc-plugin-annobin-12.2.1-3.fc38.x86_64                                       
  glibc-devel-2.36.9000-13.fc38.x86_64                                          
  glibc-headers-x86-2.36.9000-13.fc38.noarch                                    
  guile22-2.2.7-6.fc38.x86_64                                                   
  jsoncpp-1.9.5-3.fc37.x86_64                                                   
  kernel-headers-6.1.0-0.rc4.git0.1.fc38.x86_64                                 
  libb2-0.98.1-7.fc38.x86_64                                                    
  libcutl-1.10.0-25.fc38.x86_64                                                 
  libgfortran-12.2.1-3.fc38.x86_64                                              
  libicu-71.1-2.fc38.x86_64                                                     
  libicu-devel-71.1-2.fc38.x86_64                                               
  libmpc-1.2.1-5.fc38.x86_64                                                    
  libquadmath-12.2.1-3.fc38.x86_64                                              
  libquadmath-devel-12.2.1-3.fc38.x86_64                                        
  libstdc++-devel-12.2.1-3.fc38.x86_64                                          
  libtirpc-devel-1.3.3-0.fc38.x86_64                                            
  libtool-ltdl-2.4.7-2.fc37.x86_64                                              
  libuv-1:1.44.2-2.fc38.x86_64                                                  
  libxcrypt-devel-4.4.30-3.fc38.x86_64                                          
  make-1:4.4-1.fc38.x86_64                                                      
  mpdecimal-2.5.1-4.fc38.x86_64                                                 
  openblas-0.3.21-3.fc38.x86_64                                                 
  openblas-openmp-0.3.21-3.fc38.x86_64                                          
  python-pip-wheel-22.2.2-2.fc38.noarch                                         
  python-setuptools-wheel-65.5.1-1.fc38.noarch                                  
  python3-3.11.0-1.fc38.x86_64                                                  
  python3-libs-3.11.0-1.fc38.x86_64                                             
  python3-numpy-1:1.23.4-1.fc38.x86_64                                          
  rhash-1.4.3-1.fc38.x86_64                                                     
  sqlite-3.39.4-1.fc38.x86_64                                                   
  sqlite-devel-3.39.4-1.fc38.x86_64                                             
  tokyocabinet-1.4.48-20.fc38.x86_64                                            
  tokyocabinet-devel-1.4.48-20.fc38.x86_64                                      
  vim-filesystem-2:9.0.828-1.fc38.noarch                                        
  xerces-c-3.2.3-7.fc38.x86_64                                                  
  xerces-c-devel-3.2.3-7.fc38.x86_64                                            
  xsd-4.1.0-0.10.a11.fc38.x86_64                                                
  zlib-devel-1.2.12-5.fc38.x86_64                                               

Complete!
Finish: build setup for percolator-3.05-10.fc38.src.rpm
Start: rpmbuild percolator-3.05-10.fc38.src.rpm
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1658448000
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.DTE6HL
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf percolator-rel-3-05
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/percolator-rel-3-05.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd percolator-rel-3-05
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ tar -xvf /builddir/build/SOURCES/yeast-01.sqt.tar.gz
yeast-01.shuffled2.sqt
yeast-01.shuffled.sqt
yeast-01.sqt
+ find . -type f -name '*.cpp' -exec chmod 0644 '{}' ';'
+ find . -type f -name '*.h' -exec chmod 0644 '{}' ';'
+ find . -type f -name '*.xx' -exec chmod 0644 '{}' ';'
+ find . -type f -name '*.txt' -exec chmod 0644 '{}' ';'
+ chmod a-x src/converters/MSToolkit/RAMP/README
+ mv src/converters/MSToolkit/RAMP/README src/converters/MSToolkit/RAMP/RAMP-README
+ mv src/converters/MSToolkit/RAMP/Readme.Mike.txt src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt
+ cp -p /builddir/build/SOURCES/percolator-RAMP_license_lgpl-2.1.txt RAMP_license_lgpl-2.1.txt
+ sed -e 's|./bin|bin|g' -i src/qvality/CMakeLists.txt
+ sed -e 's|${ELUDE_MODELS_PATH}..|${ELUDE_MODELS_PATH}|g' -i src/elude_tool/CMakeLists.txt
+ sed -e 's|${CMAKE_INSTALL_PREFIX}/share/elude/models/|${CMAKE_INSTALL_PREFIX}/share/elude|g' -i src/elude_tool/CMakeLists.txt
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.JJ1kms
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd percolator-rel-3-05
+ export 'CXXFLAGS=-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ mkdir -p percolator
+ pushd percolator
~/build/BUILD/percolator-rel-3-05/percolator ~/build/BUILD/percolator-rel-3-05
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ /usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -Wno-dev -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE=TRUE -DXML_SUPPORT:BOOL=ON '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc' -DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DTARGET_ARCH=x86_64 ..
-- The C compiler identification is GNU 12.2.1
-- The CXX compiler identification is GNU 12.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
-- 
-- -------------------------------------------------------------------------------
-- Building PERCOLATOR:
-- change a configuration variable with: cmake -D<Variable>=<Value>
-- CMAKE_INSTALL_PREFIX = /usr
-- CMAKE_BUILD_TYPE = Release
-- CMAKE_PREFIX_PATH = ../
-- XML_SUPPORT = ON
-- GOOGLE_TEST = 
-- GOOGLE_TEST_PATH = 
-- TARGET_ARCH = x86_64
-- TOOL CHAIN FILE = 
-- PROFILING = 
-- -------------------------------------------------------------------------------
-- 
-- Architecture: 
-- Checking packages:
-- Found Xerces-C: /usr/lib64/libxerces-c.so
--               : /usr/include
--        Version: 3.2.3
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE  
-- Locating CodeSynthesis library with XSDDIR set to 
-- Package CodeSynthesis XSD found: /usr/include, /usr/bin/xsdcxx
-- Found Boost: /usr/lib64/cmake/Boost-1.78.0/BoostConfig.cmake (found suitable version "1.78.0", minimum required is "1.46.0")  
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    CMAKE_Fortran_FLAGS_RELEASE
    CMAKE_INSTALL_DO_STRIP
    CMAKE_SKIP_INSTALL_RPATH
    INCLUDE_INSTALL_DIR
    LIB_INSTALL_DIR
    LIB_SUFFIX
    SHARE_INSTALL_PREFIX
    SYSCONF_INSTALL_DIR


-- Build files have been written to: /builddir/build/BUILD/percolator-rel-3-05/percolator
+ cd src
+ xsdcxx cxx-tree --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_in/13=percolatorInNs ../../src/xml/percolator_in.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_out/15=percolatorOutNs ../../src/xml/percolator_out.xsd
+ cd ..
+ /usr/bin/make -O -j2 V=1 VERBOSE=1
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-05 -B/builddir/build/BUILD/percolator-rel-3-05/percolator --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/percolator/CMakeFiles /builddir/build/BUILD/percolator-rel-3-05/percolator//CMakeFiles/progress.marks
/usr/bin/make  -f CMakeFiles/Makefile2 all
/usr/bin/make  -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/depend
/usr/bin/make  -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src /builddir/build/BUILD/percolator-rel-3-05/percolator/src/CMakeFiles/perclibrary.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
/usr/bin/make  -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
/usr/bin/make  -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[  2%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o -MF CMakeFiles/picked_protein.dir/__/Logger.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Logger.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Logger.cpp
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o -MF CMakeFiles/picked_protein.dir/__/MyException.cpp.o.d -o CMakeFiles/picked_protein.dir/__/MyException.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/MyException.cpp
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o -MF CMakeFiles/picked_protein.dir/__/Option.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Option.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Option.cpp
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[  8%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o -MF CMakeFiles/picked_protein.dir/Database.cpp.o.d -o CMakeFiles/picked_protein.dir/Database.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Database.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Database.cpp: In member function 'void PercolatorCrux::Database::print(FILE*)':
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Database.cpp:206:12: warning: unused variable 'protein' [-Wunused-variable]
  206 |   Protein* protein = NULL;
      |            ^~~~~~~
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o -MF CMakeFiles/picked_protein.dir/Peptide.cpp.o.d -o CMakeFiles/picked_protein.dir/Peptide.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Peptide.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Peptide.cpp:375:13: warning: 'bool equal_peptides(char*, PercolatorCrux::Peptide*)' defined but not used [-Wunused-function]
  375 | static bool equal_peptides(
      |             ^~~~~~~~~~~~~~
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/PeptideConstraint.cpp
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/PeptideSrc.cpp
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/percolator_in.cxx.o -MF CMakeFiles/perclibrary.dir/percolator_in.cxx.o.d -o CMakeFiles/perclibrary.dir/percolator_in.cxx.o -c /builddir/build/BUILD/percolator-rel-3-05/percolator/src/percolator_in.cxx
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -MF CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o.d -o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/PickedProteinCaller.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/PickedProteinCaller.cpp: In member function 'bool PickedProteinCaller::getProteinFragmentsAndDuplicates(std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/PickedProteinCaller.cpp:365:8: warning: unused variable 'success' [-Wunused-variable]
  365 |   bool success = true;
      |        ^~~~~~~
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[ 16%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o -MF CMakeFiles/picked_protein.dir/Protein.cpp.o.d -o CMakeFiles/picked_protein.dir/Protein.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp: In member function 'void PercolatorCrux::Protein::shuffle(PercolatorCrux::DECOY_TYPE_T)':
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp:529:9: warning: enumeration value 'PEPTIDE_REVERSE_DECOYS' not handled in switch [-Wswitch]
  529 |   switch(decoy_type){
      |         ^
In function 'PercolatorCrux::Protein::readRawSequence(_IO_FILE*, char*, unsigned int, char*, unsigned int*)',
    inlined from 'PercolatorCrux::Protein::parseProteinFastaFile(_IO_FILE*)' at /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp:366:23:
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp:505:23: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  505 |   raw_sequence[i_seq] = '\0';
      |   ~~~~~~~~~~~~~~~~~~~~^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp: In member function 'PercolatorCrux::Protein::parseProteinFastaFile(_IO_FILE*)':
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp:355:15: note: at offset 40000 into destination object 'PercolatorCrux::Protein::parseProteinFastaFile(_IO_FILE*)::buffer' of size 40000
  355 |   static char buffer[PROTEIN_SEQUENCE_LENGTH];///> The sequence to read in.
      |               ^~~~~~
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/builddir/build/BUILD/percolator-rel-3-05/src/blas/dgemv.c: In function 'dgemv_':
/builddir/build/BUILD/percolator-rel-3-05/src/blas/dgemv.c:59:45: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
   59 |     if (*m == 0 || *n == 0 || *alpha == 0.0 && *beta == 1.0) {
      |                               ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
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                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
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/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx: In constructor 'parser_impl::parser_impl()':
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:106:33: warning: 'parser_impl::gp_' will be initialized after [-Wreorder]
  106 |   std::auto_ptr<XMLGrammarPool> gp_; // (new XMLGrammarPoolImpl (mm));
      |                                 ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:102:22: warning:   'xercesc_3_2::DOMImplementation& parser_impl::dom_impl_' [-Wreorder]
  102 |   DOMImplementation& dom_impl_;
      |                      ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:144:1: warning:   when initialized here [-Wreorder]
  144 | parser_impl::parser_impl() : clean_(true),
      | ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx: In member function 'xsd::cxx::xml::dom::auto_ptr<xercesc_3_2::DOMDocument> parser_impl::start(std::istream&, const std::string&, bool, std::string, std::string, std::string, std::string, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:178:14: warning: unused variable 'n' [-Wunused-variable]
  178 |       size_t n(s.size());
      |              ^
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:170:9: warning: unused variable 'i' [-Wunused-variable]
  170 |     int i(1);
      |         ^
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 32%] Building CXX object src/CMakeFiles/perclibrary.dir/serializer.cxx.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/serializer.cxx.o -MF CMakeFiles/perclibrary.dir/serializer.cxx.o.d -o CMakeFiles/perclibrary.dir/serializer.cxx.o -c /builddir/build/BUILD/percolator-rel-3-05/src/serializer.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 29%] Building CXX object src/fido/CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/fido/CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o -MF CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o.d -o CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:8,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 33%] Building CXX object src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -MF CMakeFiles/perclibrary.dir/BaseSpline.cpp.o.d -o CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 36%] Building CXX object src/CMakeFiles/perclibrary.dir/DescriptionOfCorrect.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/DescriptionOfCorrect.cpp.o -MF CMakeFiles/perclibrary.dir/DescriptionOfCorrect.cpp.o.d -o CMakeFiles/perclibrary.dir/DescriptionOfCorrect.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/DescriptionOfCorrect.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/DescriptionOfCorrect.cpp:23:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 37%] Building CXX object src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o -MF CMakeFiles/perclibrary.dir/MassHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/MassHandler.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/MassHandler.cpp
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[ 38%] Building CXX object src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -MF CMakeFiles/perclibrary.dir/PSMDescription.cpp.o.d -o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescription.cpp
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[ 40%] Building CXX object src/CMakeFiles/perclibrary.dir/PSMDescriptionDOC.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/PSMDescriptionDOC.cpp.o -MF CMakeFiles/perclibrary.dir/PSMDescriptionDOC.cpp.o.d -o CMakeFiles/perclibrary.dir/PSMDescriptionDOC.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp:21:
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h: In constructor 'PSMDescriptionDOC::PSMDescriptionDOC()':
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:42: warning: 'PSMDescriptionDOC::retentionTime_' will be initialized after [-Wreorder]
   92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
      |                                          ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:26: warning:   'double PSMDescriptionDOC::predictedTime_' [-Wreorder]
   92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
      |                          ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp:26:1: warning:   when initialized here [-Wreorder]
   26 | PSMDescriptionDOC::PSMDescriptionDOC() :
      | ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h: In constructor 'PSMDescriptionDOC::PSMDescriptionDOC(std::string, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:42: warning: 'PSMDescriptionDOC::retentionTime_' will be initialized after [-Wreorder]
   92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
      |                                          ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:26: warning:   'double PSMDescriptionDOC::predictedTime_' [-Wreorder]
   92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
      |                          ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp:30:1: warning:   when initialized here [-Wreorder]
   30 | PSMDescriptionDOC::PSMDescriptionDOC(const string pep, const double retTime) :
      | ^~~~~~~~~~~~~~~~~
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[ 34%] Building CXX object src/fido/CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/fido/CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o -MF CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o.d -o CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/GroupPowerBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:8,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/GroupPowerBigraph.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/GroupPowerBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 44%] Building CXX object src/fido/CMakeFiles/fido.dir/Numerical.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/fido/CMakeFiles/fido.dir/Numerical.cpp.o -MF CMakeFiles/fido.dir/Numerical.cpp.o.d -o CMakeFiles/fido.dir/Numerical.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/Numerical.cpp
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[ 45%] Building CXX object src/fido/CMakeFiles/fido.dir/Random.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/fido/CMakeFiles/fido.dir/Random.cpp.o -MF CMakeFiles/fido.dir/Random.cpp.o.d -o CMakeFiles/fido.dir/Random.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/Random.cpp
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[ 46%] Building CXX object src/fido/CMakeFiles/fido.dir/Set.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/fido/CMakeFiles/fido.dir/Set.cpp.o -MF CMakeFiles/fido.dir/Set.cpp.o.d -o CMakeFiles/fido.dir/Set.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.cpp
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[ 42%] Building CXX object src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -MF CMakeFiles/perclibrary.dir/XMLInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.h:29,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.h: In constructor 'XMLInterface::XMLInterface(const std::string&, bool, bool, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.h:99:8: warning: 'XMLInterface::reportUniquePeptides_' will be initialized after [-Wreorder]
   99 |   bool reportUniquePeptides_;
      |        ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.h:93:8: warning:   'bool XMLInterface::printDecoys_' [-Wreorder]
   93 |   bool printDecoys_, printExpMass_;
      |        ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.cpp:58:1: warning:   when initialized here [-Wreorder]
   58 | XMLInterface::XMLInterface(const std::string& outputFN,
      | ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.cpp: In member function 'int XMLInterface::readAndScorePin(std::istream&, std::vector<double>&, Scores&, const std::string&, SetHandler&, SanityCheck*&, ProteinProbEstimator*, Enzyme*&)':
/builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.cpp:257:26: warning: unused variable 'numFeatures' [-Wunused-variable]
  257 |       const unsigned int numFeatures = FeatureNames::getNumFeatures();
      |                          ^~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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[ 48%] Building CXX object src/fido/CMakeFiles/fido.dir/Vector.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/fido/CMakeFiles/fido.dir/Vector.cpp.o -MF CMakeFiles/fido.dir/Vector.cpp.o.d -o CMakeFiles/fido.dir/Vector.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.cpp
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/cmake -P CMakeFiles/fido.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/cmake -E cmake_link_script CMakeFiles/fido.dir/link.txt --verbose=1
/usr/bin/ar qc libfido.a CMakeFiles/fido.dir/BasicBigraph.cpp.o CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o CMakeFiles/fido.dir/Numerical.cpp.o CMakeFiles/fido.dir/Random.cpp.o CMakeFiles/fido.dir/Set.cpp.o CMakeFiles/fido.dir/Vector.cpp.o
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/svm.cpp.o -MF CMakeFiles/perclibrary.dir/svm.cpp.o.d -o CMakeFiles/perclibrary.dir/svm.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/svm.cpp
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 49%] Building CXX object src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o -MF CMakeFiles/perclibrary.dir/SetHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/SetHandler.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp: In member function 'int SetHandler::getNumFeatures(const std::string&, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp:158:10: warning: variable 'a' set but not used [-Wunused-but-set-variable]
  158 |   double a = reader.readDouble();
      |          ^
/builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp: In member function 'void SetHandler::readPSMs(std::istream&, std::string&, bool, bool&, std::vector<OptionalField>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp:290:18: warning: unused variable 'targetIdx' [-Wunused-variable]
  290 |     unsigned int targetIdx = 0u, decoyIdx = 0u;
      |                  ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp:290:34: warning: unused variable 'decoyIdx' [-Wunused-variable]
  290 |     unsigned int targetIdx = 0u, decoyIdx = 0u;
      |                                  ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp: In member function 'int SetHandler::readAndScoreTab(std::istream&, std::vector<double>&, Scores&, SanityCheck*&)':
/builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp:489:46: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  489 |   if (hasDefaultValues && init_values.size() > numFeatures) {
      |                           ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 56%] Building CXX object src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -MF CMakeFiles/perclibrary.dir/CrossValidation.cpp.o.d -o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.h:28,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.h: In constructor 'CrossValidation::CrossValidation(bool, bool, double, double, double, double, double, int, bool, int, bool, unsigned int, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.h:101:8: warning: 'CrossValidation::trainBestPositive_' will be initialized after [-Wreorder]
  101 |   bool trainBestPositive_;
      |        ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.h:90:16: warning:   'unsigned int CrossValidation::numThreads_' [-Wreorder]
   90 |   unsigned int numThreads_;
      |                ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:32:1: warning:   when initialized here [-Wreorder]
   32 | CrossValidation::CrossValidation(bool quickValidation,
      | ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp: In member function 'int CrossValidation::preIterationSetup(Scores&, SanityCheck*, Normalizer*, FeatureMemoryPool&)':
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:106:25: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  106 |   for (int set = 0; set < numFolds_; ++set) {
      |                     ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:107:39: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  107 |     for (int nestedSet = 0; nestedSet < nestedXvalBins_; nestedSet++) {
      |                             ~~~~~~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:141:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  141 |     for (int set = 0; set < numFolds_; ++set) {
      |                       ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:145:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  145 |     for (int set = 0; set < numFolds_; ++set) {
      |                       ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp: In member function 'int CrossValidation::doStep(bool, Normalizer*, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:263:25: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  263 |   for (int set = 0; set < numFolds_; ++set) {
      |                     ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:269:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  269 |     for (int set = 0; set < numFolds_; ++set) {
      |                       ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:291:26: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  291 |    for (int set = 0; set < numFolds_; ++set) {
      |                      ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:303:42: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  303 |      for (int nestedFold = 0; nestedFold < nestedXvalBins_; ++nestedFold)
      |                               ~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:318:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<candidateCposCfrac>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  318 |    for (int pairIdx = 0; pairIdx < classWeightsPerFold_.size(); pairIdx++){
      |                          ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp: In member function 'void CrossValidation::trainCpCnPair(candidateCposCfrac&, options*, AlgIn*)':
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:343:16: warning: unused variable 'set' [-Wunused-variable]
  343 |   unsigned int set = cpCnFold.set;
      |                ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:344:16: warning: unused variable 'nestedFold' [-Wunused-variable]
  344 |   unsigned int nestedFold = cpCnFold.nestedSet;
      |                ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:356:7: warning: unused variable 'tp' [-Wunused-variable]
  356 |   int tp = 0;
      |       ^~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp: In member function 'int CrossValidation::mergeCpCnPairs(double, options*, std::vector<std::vector<Scores> >&, const std::vector<double>&, const std::vector<double>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:399:21: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  399 |   for (set = 0; set < numFolds_; ++set) {
      |                 ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:439:23: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  439 |     for (set = 0; set < numFolds_; ++set) {
      |                   ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:474:21: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  474 |   for (set = 0; set < numFolds_; ++set) {
      |                 ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp: In member function 'void CrossValidation::postIterationProcessing(Scores&, SanityCheck*)':
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:483:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  483 |     for (int set = 0; set < numFolds_; ++set) {
      |                       ~~~~^~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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[ 57%] Building CXX object src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o -MF CMakeFiles/perclibrary.dir/Enzyme.cpp.o.d -o CMakeFiles/perclibrary.dir/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Enzyme.cpp
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[ 58%] Building CXX object src/CMakeFiles/perclibrary.dir/Globals.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/Globals.cpp.o -MF CMakeFiles/perclibrary.dir/Globals.cpp.o.d -o CMakeFiles/perclibrary.dir/Globals.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Globals.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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[ 60%] Building CXX object src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o -MF CMakeFiles/perclibrary.dir/Normalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/Normalizer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Normalizer.cpp
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.cpp:21:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.cpp:24:
/builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.h: In constructor 'SanityCheck::SanityCheck()':
/builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.h:87:8: warning: 'SanityCheck::concatenatedSearch_' will be initialized after [-Wreorder]
   87 |   bool concatenatedSearch_;
      |        ^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.h:72:10: warning:   'double SanityCheck::test_fdr_' [-Wreorder]
   72 |   double test_fdr_, initial_train_fdr_;
      |          ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.cpp:31:1: warning:   when initialized here [-Wreorder]
   31 | SanityCheck::SanityCheck() :
      | ^~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 62%] Building CXX object src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/UniNormalizer.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 64%] Building CXX object src/CMakeFiles/perclibrary.dir/DataSet.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/DataSet.cpp.o -MF CMakeFiles/perclibrary.dir/DataSet.cpp.o.d -o CMakeFiles/perclibrary.dir/DataSet.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/DataSet.cpp: In member function 'void DataSet::print_features()':
/builddir/build/BUILD/percolator-rel-3-05/src/DataSet.cpp:69:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   69 |   for (int i = 0; i < getSize(); i++) {
      |                   ~~^~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 65%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureNames.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/FeatureNames.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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[ 66%] Building CXX object src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -MF CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o.d -o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 68%] Building CXX object src/CMakeFiles/perclibrary.dir/Option.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/Option.cpp.o -MF CMakeFiles/perclibrary.dir/Option.cpp.o.d -o CMakeFiles/perclibrary.dir/Option.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Option.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 54%] Building CXX object src/CMakeFiles/perclibrary.dir/Caller.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/Caller.cpp.o -MF CMakeFiles/perclibrary.dir/Caller.cpp.o.d -o CMakeFiles/perclibrary.dir/Caller.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Caller.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/Caller.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/Caller.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Caller.h: In constructor 'Caller::Caller()':
/builddir/build/BUILD/percolator-rel-3-05/src/Caller.h:103:48: warning: 'Caller::trainBestPositive_' will be initialized after [-Wreorder]
  103 |   bool reportEachIteration_, quickValidation_, trainBestPositive_,
      |                                                ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Caller.h:101:59: warning:   'unsigned int Caller::numThreads_' [-Wreorder]
  101 |   unsigned int numIterations_, maxPSMs_, nestedXvalBins_, numThreads_;
      |                                                           ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Caller.cpp:35:1: warning:   when initialized here [-Wreorder]
   35 | Caller::Caller() :
      | ^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Caller.cpp: In member function 'bool Caller::parseOptions(int, char**)':
/builddir/build/BUILD/percolator-rel-3-05/src/Caller.cpp:694:7: warning: label 'std' defined but not used [-Wunused-label]
  694 |       std:cerr << "Error: the --static option requires the --init-weights "
      |       ^~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 70%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:34,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h: In constructor 'ProteinProbEstimator::ProteinProbEstimator(bool, double, bool, std::string, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:238:16: warning: 'ProteinProbEstimator::absenceRatio_' will be initialized after [-Wreorder]
  238 |   double pi0_, absenceRatio_;
      |                ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:238:10: warning:   'double ProteinProbEstimator::pi0_' [-Wreorder]
  238 |   double pi0_, absenceRatio_;
      |          ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:242:16: warning: 'ProteinProbEstimator::numberTargetProteins_' will be initialized after [-Wreorder]
  242 |   unsigned int numberTargetProteins_;
      |                ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:237:8: warning:   'bool ProteinProbEstimator::usePi0_' [-Wreorder]
  237 |   bool usePi0_;
      |        ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:243:15: warning: 'ProteinProbEstimator::decoyPattern_' will be initialized after [-Wreorder]
  243 |   std::string decoyPattern_;
      |               ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:240:10: warning:   'double ProteinProbEstimator::fdr_' [-Wreorder]
  240 |   double fdr_;
      |          ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 72%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/ProteinFDRestimator.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 69%] Building CXX object src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.cpp: In static member function 'static void PosteriorEstimator::getQValuesFromPEP(const std::vector<double>&, std::vector<double>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.cpp:468:21: warning: unused variable 'queue' [-Wunused-variable]
  468 |         int nP = 1, queue = 0;
      |                     ^~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 74%] Building CXX object src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -MF CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o.d -o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PseudoRandom.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 76%] Building CXX object src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/SqtSanityCheck.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/SqtSanityCheck.cpp:17:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 77%] Building CXX object src/CMakeFiles/perclibrary.dir/ssl.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/ssl.cpp.o -MF CMakeFiles/perclibrary.dir/ssl.cpp.o.d -o CMakeFiles/perclibrary.dir/ssl.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp: In function 'void cglsFun2(int, int*, const double*, double*, int, int, double*, double*, double*, double*, double, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:86:7: warning: unused variable 'ind' [-Wunused-variable]
   86 |   int ind = 0;
      |       ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:87:10: warning: unused variable 'temp' [-Wunused-variable]
   87 |   double temp = 0.0;
      |          ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp: In function 'int CGLS(const AlgIn&, double, int, double, const vector_int*, vector_double*, vector_double*, double, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:117:19: warning: unused variable 'j' [-Wunused-variable]
  117 |   register int i, j;
      |                   ^
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp: In function 'int L2_SVM_MFN(const AlgIn&, options*, vector_double*, vector_double*, double, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:251:10: warning: unused variable 't' [-Wunused-variable]
  251 |   double t = 0.0;
      |          ^
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp: In function 'double line_search(double*, double*, double, double*, double*, const double*, int, int, double, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:364:7: warning: unused variable 'inc' [-Wunused-variable]
  364 |   int inc = 1;
      |       ^~~
In function 'Clear(options*)',
    inlined from 'Clear(options*)' at /builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:440:6:
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:442:12: warning: pointer 'opt_2(D)' used after 'operator delete[](void*)' [-Wuse-after-free]
  442 |   delete[] opt;
      |            ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:441:12: note: call to 'operator delete[](void*)' here
  441 |   delete[] opt;
      |            ^~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 78%] Building CXX object src/CMakeFiles/perclibrary.dir/EludeModel.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/EludeModel.cpp.o -MF CMakeFiles/perclibrary.dir/EludeModel.cpp.o.d -o CMakeFiles/perclibrary.dir/EludeModel.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/EludeModel.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/EludeModel.cpp:34:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 80%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o -MF CMakeFiles/perclibrary.dir/PackedVector.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedVector.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.cpp
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -MF CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PackedMatrix.cpp
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 82%] Building CXX object src/CMakeFiles/perclibrary.dir/Matrix.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/Matrix.cpp.o -MF CMakeFiles/perclibrary.dir/Matrix.cpp.o.d -o CMakeFiles/perclibrary.dir/Matrix.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Matrix.cpp
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[ 73%] Building CXX object src/CMakeFiles/perclibrary.dir/Scores.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/Scores.cpp.o -MF CMakeFiles/perclibrary.dir/Scores.cpp.o.d -o CMakeFiles/perclibrary.dir/Scores.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Scores.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/Scores.cpp:32:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.cpp: In member function 'void Scores::populateWithPSMs(SetHandler&)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.cpp:292:29: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  292 |   if (totalNumberOfTargets_ <= (unsigned)(FeatureNames::getNumFeatures() * 5)) {
      |       ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.cpp:295:28: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  295 |   if (totalNumberOfDecoys_ <= (unsigned)(FeatureNames::getNumFeatures() * 5)) {
      |       ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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[ 84%] Building CXX object src/CMakeFiles/perclibrary.dir/Logger.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/Logger.cpp.o -MF CMakeFiles/perclibrary.dir/Logger.cpp.o.d -o CMakeFiles/perclibrary.dir/Logger.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Logger.cpp
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[ 85%] Building CXX object src/CMakeFiles/perclibrary.dir/MyException.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/MyException.cpp.o -MF CMakeFiles/perclibrary.dir/MyException.cpp.o.d -o CMakeFiles/perclibrary.dir/MyException.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/MyException.cpp
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[ 88%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/ProteinScoreHolder.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinScoreHolder.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinScoreHolder.h: In constructor 'ProteinScoreHolder::ProteinScoreHolder(std::string, bool, Peptide, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinScoreHolder.h:108:8: warning: 'ProteinScoreHolder::isDecoy_' will be initialized after [-Wreorder]
  108 |   bool isDecoy_;
      |        ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinScoreHolder.h:106:7: warning:   'int ProteinScoreHolder::groupId_' [-Wreorder]
  106 |   int groupId_;
      |       ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinScoreHolder.cpp:20:1: warning:   when initialized here [-Wreorder]
   20 | ProteinScoreHolder::ProteinScoreHolder(std::string name, bool isDecoy, ProteinScoreHolder::Peptide peptide,
      | ^~~~~~~~~~~~~~~~~~
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[ 86%] Building CXX object src/CMakeFiles/perclibrary.dir/FidoInterface.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/FidoInterface.cpp.o -MF CMakeFiles/perclibrary.dir/FidoInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/FidoInterface.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:34,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.h:20,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.h: In constructor 'FidoInterface::FidoInterface(double, double, double, bool, bool, bool, unsigned int, double, double, double, double, bool, std::string, bool, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.h:110:10: warning: 'FidoInterface::mseThreshold_' will be initialized after [-Wreorder]
  110 |   double mseThreshold_;
      |          ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.h:106:8: warning:   'bool FidoInterface::doGridSearch_' [-Wreorder]
  106 |   bool doGridSearch_;
      |        ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp:76:1: warning:   when initialized here [-Wreorder]
   76 | FidoInterface::FidoInterface(double alpha, double beta, double gamma,
      | ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp: In member function 'double FidoInterface::estimatePriors(Scores&)':
/builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp:132:10: warning: variable 'prior' set but not used [-Wunused-but-set-variable]
  132 |   double prior, prior2, prior3, prior4;
      |          ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp: In member function 'void FidoInterface::getEstimated_and_Empirical_FDR(const std::vector<std::vector<std::__cxx11::basic_string<char> > >&, const std::vector<double>&, std::vector<double>&, std::vector<double>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp:556:12: warning: unused variable 'prob' [-Wunused-variable]
  556 |     double prob = probabilities[k];
      |            ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp:558:14: warning: unused variable 'fpChange' [-Wunused-variable]
  558 |     unsigned fpChange = proteinNames[k].size() - tpChange;
      |              ^~~~~~~~
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[ 90%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/FeatureMemoryPool.cpp
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[ 89%] Building CXX object src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -MF CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:34,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.h:27,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.h: In constructor 'PickedProteinInterface::PickedProteinInterface(const std::string&, double, bool, bool, bool, double, bool, std::string&, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.h:86:10: warning: 'PickedProteinInterface::maxPeptidePval_' will be initialized after [-Wreorder]
   86 |   double maxPeptidePval_;
      |          ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.h:85:8: warning:   'bool PickedProteinInterface::reportFragmentProteins_' [-Wreorder]
   85 |   bool reportFragmentProteins_, reportDuplicateProteins_;
      |        ^~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp:22:1: warning:   when initialized here [-Wreorder]
   22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
      | ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.h:85:33: warning: 'PickedProteinInterface::reportDuplicateProteins_' will be initialized after [-Wreorder]
   85 |   bool reportFragmentProteins_, reportDuplicateProteins_;
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.h:83:26: warning:   'ProteinInferenceMethod PickedProteinInterface::protInferenceMethod_' [-Wreorder]
   83 |   ProteinInferenceMethod protInferenceMethod_;
      |                          ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp:22:1: warning:   when initialized here [-Wreorder]
   22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
      | ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp: In member function 'virtual bool PickedProteinInterface::initialize(Scores&, const Enzyme*)':
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp:165:36: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  165 |     if (total_non_enzymatic_flanks > peptideScores.size()) {
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp: In member function 'virtual void PickedProteinInterface::computeProbabilities(const std::string&)':
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp:344:13: warning: unused variable 'significantPeptides' [-Wunused-variable]
  344 |         int significantPeptides = 0;
      |             ^~~~~~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/cmake -P CMakeFiles/perclibrary.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/perclibrary.dir/link.txt --verbose=1
/usr/bin/ar qc libperclibrary.a CMakeFiles/perclibrary.dir/percolator_in.cxx.o CMakeFiles/perclibrary.dir/percolator_out.cxx.o CMakeFiles/perclibrary.dir/parser.cxx.o CMakeFiles/perclibrary.dir/serializer.cxx.o CMakeFiles/perclibrary.dir/BaseSpline.cpp.o CMakeFiles/perclibrary.dir/DescriptionOfCorrect.cpp.o CMakeFiles/perclibrary.dir/MassHandler.cpp.o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o CMakeFiles/perclibrary.dir/PSMDescriptionDOC.cpp.o CMakeFiles/perclibrary.dir/ResultHolder.cpp.o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o CMakeFiles/perclibrary.dir/SetHandler.cpp.o CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o CMakeFiles/perclibrary.dir/svm.cpp.o CMakeFiles/perclibrary.dir/Caller.cpp.o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o CMakeFiles/perclibrary.dir/Enzyme.cpp.o CMakeFiles/perclibrary.dir/Globals.cpp.o CMakeFiles/perclibrary.dir/Normalizer.cpp.o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o CMakeFiles/perclibrary.dir/DataSet.cpp.o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o CMakeFiles/perclibrary.dir/Option.cpp.o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o CMakeFiles/perclibrary.dir/Scores.cpp.o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o CMakeFiles/perclibrary.dir/ssl.cpp.o CMakeFiles/perclibrary.dir/EludeModel.cpp.o CMakeFiles/perclibrary.dir/PackedVector.cpp.o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o CMakeFiles/perclibrary.dir/Matrix.cpp.o CMakeFiles/perclibrary.dir/Logger.cpp.o CMakeFiles/perclibrary.dir/MyException.cpp.o CMakeFiles/perclibrary.dir/FidoInterface.cpp.o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o
/usr/bin/ranlib libperclibrary.a
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src/qvality /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src/qvality /builddir/build/BUILD/percolator-rel-3-05/percolator/src/qvality/CMakeFiles/qvality.dir/DependInfo.cmake --color=
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src /builddir/build/BUILD/percolator-rel-3-05/percolator/src/CMakeFiles/percolator.dir/DependInfo.cmake --color=
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 96%] Building CXX object src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/qvality && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o -MF CMakeFiles/qvality.dir/qvality_main.cpp.o.d -o CMakeFiles/qvality.dir/qvality_main.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/qvality/qvality_main.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 97%] Building CXX object src/CMakeFiles/percolator.dir/main.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/percolator.dir/main.cpp.o -MF CMakeFiles/percolator.dir/main.cpp.o.d -o CMakeFiles/percolator.dir/main.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/main.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/Caller.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/main.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 98%] Linking CXX executable qvality
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/qvality && /usr/bin/cmake -E cmake_link_script CMakeFiles/qvality.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -rdynamic CMakeFiles/qvality.dir/qvality_main.cpp.o -o qvality   -L/builddir/build/BUILD/percolator-rel-3-05/percolator/src  ../libperclibrary.a ../fido/libfido.a 
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/percolator.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -rdynamic CMakeFiles/percolator.dir/main.cpp.o -o percolator  libperclibrary.a blas/libblas.a fido/libfido.a picked_protein/libpicked_protein.a -lxerces-c -lstdc++ 
In function 'readRawSequence',
    inlined from 'parseProteinFastaFile' at /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp:366:23:
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp:505:23: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  505 |   raw_sequence[i_seq] = '\0';
      |                       ^
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp: In member function 'parseProteinFastaFile':
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp:355:15: note: at offset 40000 into destination object 'buffer' of size 40000
  355 |   static char buffer[PROTEIN_SEQUENCE_LENGTH];///> The sequence to read in.
      |               ^
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make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[100%] Built target percolator
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/percolator/CMakeFiles 0
+ popd
~/build/BUILD/percolator-rel-3-05
+ mkdir -p fido
+ pushd fido
~/build/BUILD/percolator-rel-3-05/fido ~/build/BUILD/percolator-rel-3-05
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ /usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -Wno-dev -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE=TRUE -DCMAKE_BUILD_TYPE:STRING=Release -DTokyoCabinet_INCLUDE_DIR=/usr/include -DTokyoCabinet_LIBRARY=/usr/lib64/libtokyocabinet.so '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc' -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DTARGET_ARCH=x86_64 ../src/fido
-- The C compiler identification is GNU 12.2.1
-- The CXX compiler identification is GNU 12.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    CMAKE_C_FLAGS_RELEASE
    CMAKE_EXE_LINKER_FLAGS_RELEASE
    CMAKE_Fortran_FLAGS_RELEASE
    CMAKE_INSTALL_DO_STRIP
    CMAKE_SKIP_INSTALL_RPATH
    CMAKE_SKIP_RPATH
    INCLUDE_INSTALL_DIR
    LIB_INSTALL_DIR
    LIB_SUFFIX
    SHARE_INSTALL_PREFIX
    SYSCONF_INSTALL_DIR
    TARGET_ARCH
    TokyoCabinet_INCLUDE_DIR
    TokyoCabinet_LIBRARY


-- Build files have been written to: /builddir/build/BUILD/percolator-rel-3-05/fido
+ /usr/bin/make -O -j2 V=1 VERBOSE=1
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-05/src/fido -B/builddir/build/BUILD/percolator-rel-3-05/fido --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/fido/CMakeFiles /builddir/build/BUILD/percolator-rel-3-05/fido//CMakeFiles/progress.marks
/usr/bin/make  -f CMakeFiles/Makefile2 all
/usr/bin/make  -f CMakeFiles/fido.dir/build.make CMakeFiles/fido.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
cd /builddir/build/BUILD/percolator-rel-3-05/fido && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/fido /builddir/build/BUILD/percolator-rel-3-05/src/fido /builddir/build/BUILD/percolator-rel-3-05/fido /builddir/build/BUILD/percolator-rel-3-05/fido /builddir/build/BUILD/percolator-rel-3-05/fido/CMakeFiles/fido.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
/usr/bin/make  -f CMakeFiles/fido.dir/build.make CMakeFiles/fido.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
[ 12%] Building CXX object CMakeFiles/fido.dir/BasicGroupBigraph.o
/usr/bin/g++  -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/BasicGroupBigraph.o -MF CMakeFiles/fido.dir/BasicGroupBigraph.o.d -o CMakeFiles/fido.dir/BasicGroupBigraph.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:8,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.cpp:4:
../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
../src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
../src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
../src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
../src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
../src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
../src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
../src/Scores.h: At global scope:
../src/Scores.h:76:32: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   76 | struct lexicOrderProb : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
                 from /usr/include/c++/12/bits/locale_classes.h:40,
                 from /usr/include/c++/12/bits/ios_base.h:41,
                 from /usr/include/c++/12/ios:42,
                 from /usr/include/c++/12/ostream:38,
                 from /usr/include/c++/12/iostream:39,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:11,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/HashTable.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/ReplicateIndexer.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:7:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:99:37: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   99 | struct OrderScanMassCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                     ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:108:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  108 | struct OrderScanMassLabelCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                          ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:119:32: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  119 | struct OrderScanLabel : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:127:38: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  127 | struct UniqueScanMassCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                      ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:133:43: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  133 | struct UniqueScanMassLabelCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                           ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:139:33: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  139 | struct UniqueScanLabel : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                 ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
[ 25%] Building CXX object CMakeFiles/fido.dir/BasicBigraph.o
/usr/bin/g++  -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/BasicBigraph.o -MF CMakeFiles/fido.dir/BasicBigraph.o.d -o CMakeFiles/fido.dir/BasicBigraph.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.cpp:4:
../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
../src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
../src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
../src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
../src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
../src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
../src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
../src/Scores.h: At global scope:
../src/Scores.h:76:32: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   76 | struct lexicOrderProb : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
                 from /usr/include/c++/12/bits/locale_classes.h:40,
                 from /usr/include/c++/12/bits/ios_base.h:41,
                 from /usr/include/c++/12/ios:42,
                 from /usr/include/c++/12/istream:38,
                 from /usr/include/c++/12/fstream:38,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:4:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:99:37: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   99 | struct OrderScanMassCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                     ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:108:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  108 | struct OrderScanMassLabelCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                          ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:119:32: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  119 | struct OrderScanLabel : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:127:38: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  127 | struct UniqueScanMassCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                      ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:133:43: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  133 | struct UniqueScanMassLabelCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                           ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:139:33: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  139 | struct UniqueScanLabel : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                 ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
[ 50%] Building CXX object CMakeFiles/fido.dir/Numerical.o
/usr/bin/g++  -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/Numerical.o -MF CMakeFiles/fido.dir/Numerical.o.d -o CMakeFiles/fido.dir/Numerical.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/Numerical.cpp
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/usr/bin/g++  -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/Random.o -MF CMakeFiles/fido.dir/Random.o.d -o CMakeFiles/fido.dir/Random.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/Random.cpp
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[ 75%] Building CXX object CMakeFiles/fido.dir/Set.o
/usr/bin/g++  -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/Set.o -MF CMakeFiles/fido.dir/Set.o.d -o CMakeFiles/fido.dir/Set.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.cpp
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[ 37%] Building CXX object CMakeFiles/fido.dir/GroupPowerBigraph.o
/usr/bin/g++  -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/GroupPowerBigraph.o -MF CMakeFiles/fido.dir/GroupPowerBigraph.o.d -o CMakeFiles/fido.dir/GroupPowerBigraph.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/GroupPowerBigraph.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:8,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/GroupPowerBigraph.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/GroupPowerBigraph.cpp:4:
../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
../src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
../src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
../src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
../src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
../src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
../src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
../src/Scores.h: At global scope:
../src/Scores.h:76:32: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   76 | struct lexicOrderProb : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
                 from /usr/include/c++/12/bits/locale_classes.h:40,
                 from /usr/include/c++/12/bits/ios_base.h:41,
                 from /usr/include/c++/12/ios:42,
                 from /usr/include/c++/12/ostream:38,
                 from /usr/include/c++/12/iostream:39,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:11,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/HashTable.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/ReplicateIndexer.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:7:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:99:37: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   99 | struct OrderScanMassCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                     ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:108:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  108 | struct OrderScanMassLabelCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                          ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:119:32: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  119 | struct OrderScanLabel : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:127:38: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  127 | struct UniqueScanMassCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                      ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:133:43: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  133 | struct UniqueScanMassLabelCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                           ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:139:33: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  139 | struct UniqueScanLabel : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                 ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
[ 87%] Building CXX object CMakeFiles/fido.dir/Vector.o
/usr/bin/g++  -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/Vector.o -MF CMakeFiles/fido.dir/Vector.o.d -o CMakeFiles/fido.dir/Vector.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.cpp
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/usr/bin/cmake -P CMakeFiles/fido.dir/cmake_clean_target.cmake
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/usr/bin/ar qc libfido.a CMakeFiles/fido.dir/BasicBigraph.o CMakeFiles/fido.dir/BasicGroupBigraph.o CMakeFiles/fido.dir/GroupPowerBigraph.o CMakeFiles/fido.dir/Numerical.o CMakeFiles/fido.dir/Random.o CMakeFiles/fido.dir/Set.o CMakeFiles/fido.dir/Vector.o
/usr/bin/ranlib libfido.a
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[100%] Built target fido
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/fido/CMakeFiles 0
+ popd
~/build/BUILD/percolator-rel-3-05
+ mkdir -p converters
+ pushd converters
~/build/BUILD/percolator-rel-3-05/converters ~/build/BUILD/percolator-rel-3-05
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ /usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -Wno-dev -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE=TRUE '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc' -DCMAKE_BUILD_TYPE:STRING=Release -DPERCOLATOR-CONVERTERS_BINARY_DIR:STATIC=converters -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DTokyoCabinet_INCLUDE_DIR=/usr/include -DTokyoCabinet_LIBRARY=/usr/lib64/libtokyocabinet.so -DSERIALIZE=TokyoCabinet -DTARGET_ARCH=x86_64 ../src/converters
-- The C compiler identification is GNU 12.2.1
-- The CXX compiler identification is GNU 12.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
-- 
-- -------------------------------------------------------------------------------
-- Building PERCOLATOR-CONVERTERS:
-- change a configuration variable with: cmake -D<Variable>=<Value>
-- Indicate the type of XML serialization scheme : 
		  -DSERIALIZE="Boost" or -DSERIALIZE="TokyoCabinet" 
		  or -DSERIALIZE="LevelDB".
		  By setting up the variable SERIALIZE to either Boost 
		  or TokyoCabinet or LevelDB you will choose the serialization 
		  scheme that will be used to build Converters.
		  Boost serialization option will be used as default if no option is given.
-- CMAKE_INSTALL_PREFIX = /usr
-- CMAKE_BUILD_TYPE = Release
-- XML_SUPPORT = ON
-- PERCOLATOR_SOURCE_DIR = /builddir/build/BUILD/percolator-rel-3-05/src/converters/../..
-- CMAKE_PREFIX_PATH = ../
-- TARGET_ARCH = x86_64
-- TOOL CHAIN FILE = 
-- SERIALIZE = TokyoCabinet
-- PROFILING = 
-- Using Tokyo Cabinet Serialization scheme
-- -------------------------------------------------------------------------------
-- 
-- Architecture: 
-- Checking packages..
-- Found Xerces-C: /usr/lib64/libxerces-c.so
--               : /usr/include
--        Version: 3.2.3
-- Package CodeSynthesis XSD found: /usr/include
-- Found TokyoCabinet: /usr/lib64/libtokyocabinet.so  
-- Package Tokyo Cabinet found : /usr/include
-- Found BZip2: /usr/lib64/libbz2.so  
-- Looking for BZ2_bzCompressInit in /usr/lib64/libbz2.so
-- Looking for BZ2_bzCompressInit in /usr/lib64/libbz2.so - found
-- Bzip2 found
-- Found Boost: /usr/lib64/cmake/Boost-1.78.0/BoostConfig.cmake (found suitable version "1.78.0", minimum required is "1.46.0") found components: filesystem system 
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE  
-- Generating classes from xsd-schema using CodeSynthesis
-- Generating /builddir/build/BUILD/percolator-rel-3-05/converters/gaml_tandem1.0.cxx;/builddir/build/BUILD/percolator-rel-3-05/converters/gaml_tandem1.0.hxx
-- SQL Lite 3 found: /usr/include
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.12") 
-- ZLIB found: /usr/include, /usr/lib64/libz.so
-- Using FragSpectrumScanDatabaseTokyodb.cpp
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    CMAKE_Fortran_FLAGS_RELEASE
    CMAKE_INSTALL_DO_STRIP
    CMAKE_SKIP_INSTALL_RPATH
    INCLUDE_INSTALL_DIR
    LIB_INSTALL_DIR
    LIB_SUFFIX
    SHARE_INSTALL_PREFIX
    SYSCONF_INSTALL_DIR


-- Build files have been written to: /builddir/build/BUILD/percolator-rel-3-05/converters
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_in/13=percolatorInNs ../src/xml/percolator_in.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_out/15=percolatorOutNs ../src/xml/percolator_out.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://psidev.info/psi/pi/mzIdentML/1.1=mzIdentML_ns ../src/xml/mzIdentML1.1.0.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://www.bioml.com/gaml/=gaml_tandem_ns ../src/xml/gaml_tandem1.0.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://www.thegpm.org/TANDEM/2011.12.01.1=tandem_ns --namespace-map =tandem_ns --namespace-map http://www.bioml.com/gaml/=gaml_tandem_ns ../src/xml/tandem2011.12.01.1.xsd
+ /usr/bin/make -O -j2 V=1 VERBOSE=1
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-05/src/converters -B/builddir/build/BUILD/percolator-rel-3-05/converters --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles /builddir/build/BUILD/percolator-rel-3-05/converters//CMakeFiles/progress.marks
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/generate_perc_xsdfiles.dir/DependInfo.cmake --color=
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cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit/RAMP && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__  -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp_base64.cpp.o -MF CMakeFiles/RAMP.dir/ramp_base64.cpp.o.d -o CMakeFiles/RAMP.dir/ramp_base64.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp_base64.cpp
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[  9%] Building CXX object MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit/RAMP && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__  -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp.cpp.o -MF CMakeFiles/RAMP.dir/ramp.cpp.o.d -o CMakeFiles/RAMP.dir/ramp.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1698:13: warning: variable 'err' set but not used [-Wunused-but-set-variable]
 1698 |         int err;
      |             ^~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:34:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'RAMPFILE* rampOpenFile(const char*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:188:16: note: in expansion of macro 'ramp_fgets'
  188 |         (void) ramp_fgets(buf, sizeof(buf) - 1, result);
      |                ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'ramp_fileoffset_t getIndexOffset(RAMPFILE*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:118:41: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  118 | #define ramp_fread(buf,len,handle) fread(buf,1,len,(handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:343:3: note: in expansion of macro 'ramp_fread'
  343 |   ramp_fread(indexOffsetTemp, sizeof(indexOffsetTemp), pFI);
      |   ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'ramp_fileoffset_t* readIndex(RAMPFILE*, ramp_fileoffset_t, int*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:509:18: note: in expansion of macro 'ramp_fgets'
  509 |           (void) ramp_fgets(buf, SIZE_BUF, pFI);
      |                  ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:541:18: note: in expansion of macro 'ramp_fgets'
  541 |           (void) ramp_fgets(buf, SIZE_BUF, pFI);
      |                  ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:575:16: note: in expansion of macro 'ramp_fgets'
  575 |         (void) ramp_fgets(buf, SIZE_BUF, pFI);
      |                ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'void readHeader(RAMPFILE*, ramp_fileoffset_t, ScanHeaderStruct*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:967:18: note: in expansion of macro 'ramp_fgets'
  967 |           (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |                  ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:984:18: note: in expansion of macro 'ramp_fgets'
  984 |           (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |                  ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'int readMsLevel(RAMPFILE*, ramp_fileoffset_t)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1056:10: note: in expansion of macro 'ramp_fgets'
 1056 |   (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |          ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1058:12: note: in expansion of macro 'ramp_fgets'
 1058 |     (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |            ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:118:41: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  118 | #define ramp_fread(buf,len,handle) fread(buf,1,len,(handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1479:11: note: in expansion of macro 'ramp_fread'
 1479 |           ramp_fread(pData + partial, (int)(peaksLen - partial), pFI);
      |           ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1571:14: note: in expansion of macro 'ramp_fgets'
 1571 |       (void) ramp_fgets(buf, sizeof(buf) - 1, pFI);
      |              ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1573:16: note: in expansion of macro 'ramp_fgets'
 1573 |         (void) ramp_fgets(buf, sizeof(buf) - 1, pFI);
      |                ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1626:18: note: in expansion of macro 'ramp_fgets'
 1626 |           (void) ramp_fgets(buf, sizeof(buf) - 1 , pFI);
      |                  ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:118:41: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  118 | #define ramp_fread(buf,len,handle) fread(buf,1,len,(handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1658:9: note: in expansion of macro 'ramp_fread'
 1658 |         ramp_fread(pData + partial, peaksLen - partial, pFI);
      |         ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'void readMSRun(RAMPFILE*, RunHeaderStruct*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1792:10: note: in expansion of macro 'ramp_fgets'
 1792 |   (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |          ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1795:12: note: in expansion of macro 'ramp_fgets'
 1795 |     (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |            ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1816:12: note: in expansion of macro 'ramp_fgets'
 1816 |     (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |            ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'InstrumentStruct* getInstrumentStruct(RAMPFILE*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1926:10: note: in expansion of macro 'ramp_fgets'
 1926 |   (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |          ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1933:13: note: in expansion of macro 'ramp_fgets'
 1933 |      (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |             ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1989:14: note: in expansion of macro 'ramp_fgets'
 1989 |       (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |              ^~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:123:
In function '*strchr',
    inlined from 'readPeaks(RAMPFILE*, long)' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1599:35:
/usr/include/string.h:241:27: warning: 'strchr' reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
  241 |   return __builtin_strchr (__s, __c);
      |          ~~~~~~~~~~~~~~~~~^~~~~~~~~~
In function '*strchr',
    inlined from 'readPeaks(RAMPFILE*, long)' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1613:35:
/usr/include/string.h:241:27: warning: 'strchr' reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
  241 |   return __builtin_strchr (__s, __c);
      |          ~~~~~~~~~~~~~~~~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'rampSelfTest(char*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:2050:12: warning: 'strncpy' specified bound 256 equals destination size [-Wstringop-truncation]
 2050 |     strncpy(buf, filename, sizeof(buf));
      |            ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:2054:12: warning: 'strncpy' specified bound 256 equals destination size [-Wstringop-truncation]
 2054 |     strncpy(buf, filename, sizeof(buf));
      |            ^
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/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx: In constructor 'parser_impl::parser_impl()':
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:106:33: warning: 'parser_impl::gp_' will be initialized after [-Wreorder]
  106 |   std::auto_ptr<XMLGrammarPool> gp_; // (new XMLGrammarPoolImpl (mm));
      |                                 ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:102:22: warning:   'xercesc_3_2::DOMImplementation& parser_impl::dom_impl_' [-Wreorder]
  102 |   DOMImplementation& dom_impl_;
      |                      ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:144:1: warning:   when initialized here [-Wreorder]
  144 | parser_impl::parser_impl() : clean_(true),
      | ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx: In member function 'xsd::cxx::xml::dom::auto_ptr<xercesc_3_2::DOMDocument> parser_impl::start(std::istream&, const std::string&, bool, std::string, std::string, std::string, std::string, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:178:14: warning: unused variable 'n' [-Wunused-variable]
  178 |       size_t n(s.size());
      |              ^
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:170:9: warning: unused variable 'i' [-Wunused-variable]
  170 |     int i(1);
      |         ^
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cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o -MF CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o.d -o CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In function 'LazyMatrix* flip_lazy_matrix(LazyMatrix&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:21:30: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   21 |         for ( uint j = 0 ; j < lm.rows() ; j++ ) {
      |                            ~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:22:38: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   22 |                 for ( uint i = 0 ; i < lm.cols() ; i++ ) {
      |                                    ~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In copy constructor 'LazyMatrix::LazyMatrix(const self&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:56:6: warning: value computed is not used [-Wunused-value]
   56 |      *data_copies++;
      |      ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::copy_m_flip(const self&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:67:28: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'const int' [-Wsign-compare]
   67 |       for ( uint i = 0 ; i < x.nrows ; i++ ) {
      |                          ~~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::to_full_data(bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:101:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float>*>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  101 |           for ( int i = 0 ; i < m.size() ; i++ ) {
      |                             ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::to_full_data(value_type, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:115:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float>*>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  115 |           for ( int i = 0 ; i < m.size() ; i++ ) {
      |                             ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::_get_row_retain(std::vector<float>&, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:179:43: warning: variable 'b' set but not used [-Wunused-but-set-variable]
  179 |              std::vector<float>::iterator b = this->m[i]->begin();
      |                                           ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::add_val(float)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:313:31: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  313 |          for ( uint i = 0 ; i < nrows ; i++ ) {
      |                             ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::mult_val(float)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:322:31: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  322 |          for ( uint i = 0 ; i < nrows ; i++ ) {
      |                             ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::div_val(float)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:331:31: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  331 |          for ( uint i = 0 ; i < nrows ; i++ ) {
      |                             ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::set_min_val(float)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:339:26: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  339 |     for ( uint i = 0 ; i < nrows ; i++ ) {
      |                        ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::set_max_val(float)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:351:26: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  351 |     for ( uint i = 0 ; i < nrows ; i++ ) {
      |                        ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::column_shift(int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:369:23: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  369 |   for ( uint i = 0 ;i < rows() ; i++ ) {
      |                     ~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:370:26: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  370 |     for ( uint j = 0 ; j < cols() ; j++ ) {
      |                        ~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:373:21: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  373 |       if ( dest_idx >= cols() ) break;
      |            ~~~~~~~~~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::linear_shift(int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:389:25: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  389 |     for ( uint i = 0; i < shift ; i++ ) {
      |                       ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:393:29: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  393 |     for ( uint i = shift; i < nrows; i++ ) {
      |                           ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:412:39: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  412 |     for ( uint i = nrows - offset ; i < nrows; i++ ) {
      |                                     ~~^~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
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[ 38%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o -MF CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSConvertFile.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 40%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSObject.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSObject.cpp.o -MF CMakeFiles/MSToolkit.dir/MSObject.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSObject.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSObject.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSObject.cpp: In copy constructor 'MSObject::MSObject(const MSObject&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSObject.cpp:21:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Spectrum>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   21 |   for(i=0;i<m.vSpectrum->size();i++){
      |           ~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSObject.cpp: In member function 'MSObject& MSObject::operator=(const MSObject&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSObject.cpp:36:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Spectrum>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   36 |     for(i=0;i<m.vSpectrum->size();i++){
      |             ~^~~~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 41%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSReader.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSReader.cpp.o -MF CMakeFiles/MSToolkit.dir/MSReader.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'void MSReader::writeSqlite(const char*, MSObject&, char*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:634:34: warning: the address of 'MSHeader::header' will never be NULL [-Waddress]
  634 |       if(m.getHeader().header[i] != 0)
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.h:4,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.h:4,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSToolkitTypes.h:54:14: note: 'MSHeader::header' declared here
   54 |         char header[16][128];
      |              ^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'void MSReader::appendFile(Spectrum&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:916:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  916 |           for(int i=0; i<chgs.size(); i++)
      |                        ~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:750:7: warning: variable 'err' set but not used [-Wunused-but-set-variable]
  750 |   int err;
      |       ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:756:9: warning: variable 'sizeM' set but not used [-Wunused-but-set-variable]
  756 |   uLong sizeM;
      |         ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:757:9: warning: variable 'sizeI' set but not used [-Wunused-but-set-variable]
  757 |   uLong sizeI;
      |         ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'bool MSReader::executeSqlStmt(Spectrum&, char*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1187:7: warning: unused variable 'charge' [-Wunused-variable]
 1187 |   int charge=-1;
      |       ^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'void MSReader::writeCompressSpec(FILE*, Spectrum&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1610:13: warning: variable 'err' set but not used [-Wunused-but-set-variable]
 1610 |         int err;
      |             ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1616:15: warning: variable 'sizeM' set but not used [-Wunused-but-set-variable]
 1616 |         uLong sizeM;
      |               ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1617:15: warning: variable 'sizeI' set but not used [-Wunused-but-set-variable]
 1617 |         uLong sizeI;
      |               ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'int MSReader::openFile(const char*, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:101:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  101 |       fread(&iFType,4,1,fileIn);
      |       ~~~~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:102:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  102 |       fread(&iVersion,4,1,fileIn);
      |       ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:103:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  103 |                         fread(&header,sizeof(MSHeader),1,fileIn);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'bool MSReader::readFile(const char*, bool, Spectrum&, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:189:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  189 |                 fread(&i,4,1,fileIn);
      |                 ~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:191:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  191 |                 fread(&i,4,1,fileIn);
      |                 ~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:207:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  207 |       fread(&z.z,4,1,fileIn);
      |       ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:208:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  208 |       fread(&z.mz,8,1,fileIn);
      |       ~~~~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:213:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  213 |       fread(&ez.z,4,1,fileIn);
      |       ~~~~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:214:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  214 |       fread(&ez.mh,8,1,fileIn);
      |       ~~~~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:215:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  215 |       fread(&ez.pRTime,4,1,fileIn);
      |       ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:216:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  216 |       fread(&ez.pArea,4,1,fileIn);
      |       ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:239:20: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  239 |               fread(&p.mz,8,1,fileIn);
      |               ~~~~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:240:20: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  240 |               fread(&p.intensity,4,1,fileIn);
      |               ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:280:20: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  280 |               fgets(tstr,256,fileIn);
      |               ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:285:20: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  285 |               fgets(tstr,256,fileIn);
      |         make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
      ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:297:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  297 |         fgets(tstr,256,fileIn);
      |         ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:347:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  347 |                 fgets(tstr,256,fileIn);
      |                 ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:374:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  374 |                 fgets(tstr,256,fileIn);
      |                 ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:377:20: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  377 |               fgets(tstr,256,fileIn);
      |               ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:400:24: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  400 |                   fgets(tstr,256,fileIn);
      |                   ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:405:21: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
  405 |               fscanf(fileIn,"%lf %f\n",&p.mz,&p.intensity);
      |               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:411:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  411 |         fgets(tstr,256,fileIn);
      |         ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'void MSReader::readCompressSpec(FILE*, MSScanInfo&, Spectrum&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1669:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1669 |         fread(&i,4,1,fileIn);
      |         ~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1671:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1671 |         fread(&i,4,1,fileIn);
      |         ~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1677:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1677 |         fread(compr,mzLen,1,fileIn);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1684:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1684 |         fread(compr,intensityLen,1,fileIn);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'void MSReader::readSpecHeader(FILE*, MSScanInfo&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1882:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1882 |   fread(&ms.scanNumber[0],4,1,fileIn);
      |   ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1884:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1884 |   fread(&ms.scanNumber[1],4,1,fileIn);
      |   ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1885:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1885 |   fread(&ms.mz,8,1,fileIn);
      |   ~~~~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1886:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1886 |   fread(&ms.rTime,4,1,fileIn);
      |   ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1889:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1889 |     fread(&ms.BPI,4,1,fileIn);
      |     ~~~~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1890:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1890 |     fread(&ms.BPM,8,1,fileIn);
      |     ~~~~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1891:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1891 |     fread(&ms.convA,8,1,fileIn);
      |     ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1892:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1892 |     fread(&ms.convB,8,1,fileIn);
      |     ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1893:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1893 |     fread(&ms.TIC,8,1,fileIn);
      |     ~~~~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1894:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1894 |     fread(&ms.IIT,4,1,fileIn);
      |     ~~~~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1897:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1897 |   fread(&ms.numZStates,4,1,fileIn);
      |   ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1899:24: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1899 |   if(iVersion>=3) fread(&ms.numEZStates,4,1,fileIn);
      |                   ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1902:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1902 |   fread(&ms.numDataPoints,4,1,fileIn);
      |   ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'MSFileFormat MSReader::checkFileFormat(const char*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1952:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1952 |   fread(&i,4,1,f);
      |   ~~~~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1953:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1953 |   fread(&iVersion,4,1,f);
      |   ~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:906,
                 from /usr/include/c++/12/cstdio:42,
                 from /usr/include/c++/12/parallel/compiletime_settings.h:33,
                 from /usr/include/c++/12/parallel/parallel.h:37,
                 from /usr/include/c++/12/parallel/base.h:40,
                 from /usr/include/c++/12/parallel/algobase.h:40,
                 from /usr/include/c++/12/bits/stl_algobase.h:2225,
                 from /usr/include/c++/12/vector:60,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.h:5:
In function 'sprintf',
    inlined from 'MSReader::appendFile(Spectrum&)' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:920:15:
/usr/include/bits/stdio2.h:30:34: warning: 'lastScanID' may be used uninitialized [-Wmaybe-uninitialized]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'MSReader::appendFile(Spectrum&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:853:7: note: 'lastScanID' was declared here
  853 |   int lastScanID;
      |       ^~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 43%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o -MF CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSSingleScan.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 45%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o -MF CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSTAllRT.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSTAllRT.cpp: In function 'int main(int, char**)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSTAllRT.cpp:51:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   51 |   for ( int i = 0 ; i < rts.size() ; i++ ) {
      |                     ~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSTAllRT.cpp:26:22: warning: variable 'ff' set but not used [-Wunused-but-set-variable]
   26 |         MSFileFormat ff;
      |                      ^~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 47%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o -MF CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSTDemo.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 49%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSWarper.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSWarper.cpp.o -MF CMakeFiles/MSToolkit.dir/MSWarper.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSWarper.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSWarper.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSWarper.cpp:17:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'std::pair<float, float> msmat::get_transition_by_idx() const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:517:3: warning: no return statement in function returning non-void [-Wreturn-type]
  517 |   }
      |   ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'int msmat::get_idx_by_transition(std::pair<float, float>) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:519:3: warning: no return statement in function returning non-void [-Wreturn-type]
  519 |   }
      |   ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_scans::msmat_scans()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:600:15: warning: unused variable 'a' [-Wunused-variable]
  600 |           int a = 3;
      |               ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_chroms::msmat_chroms()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:703:9: warning: unused variable 'a' [-Wunused-variable]
  703 |     int a  = 3;
      |         ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSWarper.cpp: In function 'int main(int, char**)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSWarper.cpp:87:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<const char*>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   87 |   for ( int f_idx = 0; f_idx < ms1_file_names.size() ; f_idx++ ) {
      |                        ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:812:12: warning: 'int test_msmat_time_interp(msmat*)' declared 'static' but never defined [-Wunused-function]
  812 | static int test_msmat_time_interp( msmat * msmat_f );
      |            ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:813:12: warning: 'int test_msmat_sg_test(msmat*)' declared 'static' but never defined [-Wunused-function]
  813 | static int test_msmat_sg_test( msmat * msmat_fh);
      |            ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:814:12: warning: 'int test_msmat_output(msmat*, char*)' declared 'static' but never defined [-Wunused-function]
  814 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
      |            ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:815:16: warning: 'msmat* test_msmat(int, char**)' declared 'static' but never defined [-Wunused-function]
  815 | static msmat * test_msmat(int argc, char ** argv);
      |                ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:818:13: warning: 'void output_bp_chrom(msmat&, char*)' declared 'static' but never defined [-Wunused-function]
  818 | static void output_bp_chrom( msmat & m , char * fname);
      |             ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:819:17: warning: 'msmat* msmat_from_fh(FILE*, sparse_level)' declared 'static' but never defined [-Wunused-function]
  819 | static msmat *  msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA );
      |                 ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:820:16: warning: 'msmat* msmat_from_thevoid(const std::vector<float>&, const std::vector<float>&, std::vector<std::vector<float> >&, bool)' declared 'static' but never defined [-Wunused-function]
  820 | static msmat * msmat_from_thevoid ( const std::vector<float> & mzs, const std::vector<float> & rts, std::vector < std::vector< float > > & chroms , bool as_scans = true );
      |                ^~~~~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:48:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_base.H:69:21: warning: 'valid_fields' defined but not used [-Wunused-variable]
   69 | const static char * valid_fields[] = {
      |                     ^~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 50%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/Spectrum.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/Spectrum.cpp.o -MF CMakeFiles/MSToolkit.dir/Spectrum.cpp.o.d -o CMakeFiles/MSToolkit.dir/Spectrum.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp: In member function 'Spectrum& Spectrum::operator=(const Spectrum&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp:81:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Peak_T>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   81 |     for(i=0;i<s.vPeaks->size();i++){
      |             ~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp:85:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<EZState>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   85 |     for(i=0;i<s.vEZ->size();i++){
      |             ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp:89:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ZState>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   89 |     for(i=0;i<s.vZ->size();i++){
      |             ~^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp: In member function 'bool Spectrum::getRawFilter(char*, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp:282:8: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  282 |   if(sz<strlen(rawFilter)) {
      |      ~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp: In member function 'float Spectrum::getTotalIntensity()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp:389:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Peak_T>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  389 |   for(int i=0; i<vPeaks->size(); i++)
      |                ~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp: In member function 'void Spectrum::setPeaks(std::vector<Peak_T>)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp:428:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Peak_T>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  428 |   for(int i=0; i<peaks.size(); i++)
      |                ~^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp: In member function 'void Spectrum::printMe()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp:453:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Peak_T>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  453 |   for(int i=0; i<vPeaks->size(); i++)
      |                ~^~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 52%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/crawutils.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/crawutils.cpp.o -MF CMakeFiles/MSToolkit.dir/crawutils.cpp.o.d -o CMakeFiles/MSToolkit.dir/crawutils.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp: In function 'void crawutils::rankties(std::vector<float>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:261:9: warning: unused variable 'start_idx' [-Wunused-variable]
  261 |     int start_idx = -1;
      |         ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:262:9: warning: unused variable 'stop_idx' [-Wunused-variable]
  262 |     int stop_idx = -1;
      |         ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp: In function 'void crawutils::rank_by_pos_ties(const std::vector<std::pair<float, int> >&, std::vector<float>&, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:354:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<float, int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  354 |       if ( ( i != (sorted_by_i.size() ) ) && ( sorted_by_i[i].first == last_val) ) {
      |              ~~^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:346:9: warning: unused variable 'last_rank' [-Wunused-variable]
  346 |     int last_rank = -1;
      |         ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp: In function 'int crawutils::idx_of_centroid(const std::vector<float>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:944:32: warning: comparison of integer expressions of different signedness: 'std::vector<float>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  944 |     if (cumulative_area.size() == idx)
      |         ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp: In function 'int crawutils::idx_of_centroid(const std::vector<float>&, const std::vector<float>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:990:32: warning: comparison of integer expressions of different signedness: 'std::vector<float>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  990 |     if (cumulative_area.size() == idx)
      |         ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp: In function 'int crawutils::tryptic_digester_proto(std::string, std::vector<std::__cxx11::basic_string<char> >&, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:1121:10: warning: unused variable 'last_tryp' [-Wunused-variable]
 1121 |     bool last_tryp = false;
      |          ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp: In function 'std::vector<std::pair<std::set<int>, std::set<int> > > crawutils::permute_two_groups(IdxGroupType, IdxGroupType)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:1214:8: warning: unused variable 'g2_len' [-Wunused-variable]
 1214 |    int g2_len = g2.size();
      |        ^~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
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[ 29%] Building CXX object CMakeFiles/converters.dir/mzIdentML1.1.0.cxx.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/mzIdentML1.1.0.cxx.o -MF CMakeFiles/converters.dir/mzIdentML1.1.0.cxx.o.d -o CMakeFiles/converters.dir/mzIdentML1.1.0.cxx.o -c /builddir/build/BUILD/percolator-rel-3-05/converters/mzIdentML1.1.0.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 54%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/msmat.cpp.o -MF CMakeFiles/MSToolkit.dir/msmat.cpp.o.d -o CMakeFiles/MSToolkit.dir/msmat.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:17:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'std::pair<float, float> msmat::get_transition_by_idx() const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:517:3: warning: no return statement in function returning non-void [-Wreturn-type]
  517 |   }
      |   ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'int msmat::get_idx_by_transition(std::pair<float, float>) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:519:3: warning: no return statement in function returning non-void [-Wreturn-type]
  519 |   }
      |   ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_scans::msmat_scans()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:600:15: warning: unused variable 'a' [-Wunused-variable]
  600 |           int a = 3;
      |               ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_chroms::msmat_chroms()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:703:9: warning: unused variable 'a' [-Wunused-variable]
  703 |     int a  = 3;
      |         ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'std::vector<transition_info> transition_manager::get_trans_by_precursor(float)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:37:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   37 |        for ( int i = 0 ; i < precursors.size() ; i++ )
      |                          ~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'std::vector<transition_info> transition_manager::get_trans_by_precursor_idx(int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:48:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<transition_info>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   48 |         for ( int i = 0 ; i < ti.size() ; i++ ) {
      |                           ~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In constructor 'transition_manager::transition_manager(std::vector<transition_info>)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:57:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<transition_info>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   57 |       for ( int  i = 0 ; i < transitions.size() ; i++ ) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::init_transitions_from_labels()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:86:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   86 |    for ( int i = 0 ; i < labels.size() ; i++ ) {
      |                      ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::tabular_input(std::ifstream&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:119:36: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  119 |      for ( int mz_idx = 0 ; mz_idx < this->get_num_mzs() ; mz_idx++ ) {
      |                             ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:120:38: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  120 |          for ( int c_idx = 0 ; c_idx < this->get_num_rts() ; c_idx++ ) {
      |                                ~~~~~~^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:117:10: warning: unused variable 'num_chroms' [-Wunused-variable]
  117 |      int num_chroms = this->get_num_mzs();
      |          ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:118:10: warning: unused variable 'num_rts' [-Wunused-variable]
  118 |      int num_rts = this->get_num_rts();
      |          ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::retain_dist_set(int, std::vector<int>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:228:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  228 |     for ( int i = 0 ; i < this->get_num_rts() ; i++ ) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::retain_chrom_set(int, std::vector<std::pair<int, int> >&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:247:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<int, int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  247 |     for ( int i = 1 ; i < retain_range.size() ; i++ ) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:255:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<int, int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  255 |     for ( int i = 0 ; i < delete_range.size() ; i++ ) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:237:9: warning: unused variable 'set_idx' [-Wunused-variable]
  237 |     int set_idx = 0;
      |         ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::retain_chrom(int, int, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:266:39: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  266 |   for ( int i = stop_scan_idx + 1 ; i < get_num_rts() ; i++ ) {
      |                                     ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'int msmat::check_size_from_position() const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:283:30: warning: comparison of integer expressions of different signedness: 'off64_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  283 |   if ( ( end_pos - cur_pos ) == get_num_mzs() * get_num_rts() * sizeof(float) ) {
      |        ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'int msmat::rt_to_rtidx(float) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:417:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  417 |      if ( iter_delt == rts.size() - 1 )
      |           ~~~~~~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::calc_bp_chrom()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:680:28: warning: variable 'scan_length' set but not used [-Wunused-but-set-variabmake[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
le]
  680 |   int scan_idx, num_scans, scan_length;
      |                            ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::time_interpolate(double, msmat&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1068:14: warning: variable 'dim' set but not used [-Wunused-but-set-variable]
 1068 |   matrix_dim dim = get_data_dim();
      |              ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::get_median() const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1278:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1278 |   for ( int i = 0 ; i < this->get_num_rows() ; i++ ) {
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1279:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1279 |     for ( int j = 0 ; j < this->get_num_cols() ; j++ ) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::get_avg(int) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1294:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1294 |     if ( i < 0 || i >= get_num_rts()  ) {
      |                   ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::calc_twomat_num(const msmat&, double, double, int) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1325:72: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1325 |                                      for ( int self_idx = 0 ; self_idx < get_num_rts() ; self_idx++ ) {
      |                                                               ~~~~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1327:72: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1327 |                                        if ( other_idx < 0 || other_idx >= other.get_num_rts() ) {
      |                                                              ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::calc_mat_denom(double, int) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1350:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1350 |     if ( i < 0 || i >= get_num_rts() ) {
      |                   ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::correlation_w_shift(const msmat&, int) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1368:17: warning: unused variable 'self' [-Wunused-variable]
 1368 |   const msmat & self = *this;
      |                 ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'msmat_chroms* msmat_chroms::extract_mzidx_range(int, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1422:9: warning: unused variable 'foo' [-Wunused-variable]
 1422 |     int foo = 5;
      |         ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'virtual void msmat_scans::get_chrom(int, std::vector<float>&) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1498:11: warning: unused variable 'volatile_this' [-Wunused-variable]
 1498 |   msmat * volatile_this;
      |           ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::scan_scramble()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1555:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1555 |   for ( int i = 0 ; i < get_num_rts() ; i++ ) {
      |                     ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1561:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<int, int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1561 |   for ( int i = 0 ; i < scram_cmds.size() ; i++ ) {
      |                     ~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In function 'msmat* test_msmat(int, char**)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1605:19: warning: variable 'ti_file' set but not used [-Wunused-but-set-variable]
 1605 |   FILE * o_file, *ti_file, *sg_file;
      |                   ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1605:29: warning: variable 'sg_file' set but not used [-Wunused-but-set-variable]
 1605 |   FILE * o_file, *ti_file, *sg_file;
      |                             ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In function 'msmat* msmat_from_thevoid(const std::vector<float>&, const std::vector<float>&, std::vector<std::vector<float> >&, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1746:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1746 |   for ( int i = 0 ; i < chroms.size() ; i++ ){
      |                     ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1762:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1762 |   for ( int i = 0 ; i < chroms.size() ; i++ ){
      |                     ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::decimate_mzs_by_avg(int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1828:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1828 |     new_cnt < mzs.size() ;
      |     ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::decimate_rts_by_avg(int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1858:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1858 |     new_cnt < rts.size() ;
      |     ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::decimate_mzs_by_sample(int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1880:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1880 |     new_cnt < mzs.size() ;
      |     ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::decimate_rts_by_sample(int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1898:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1898 |     new_cnt < rts.size() ;
      |     ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'bool msmat::equals_data(const msmat&, double) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1921:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1921 |   for ( int i = 0 ; i < get_num_rows() ; i++ ) {
      |                     ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::sum_abs_diffs(const msmat&) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1944:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1944 |   for ( int i = 0 ; i < get_num_rows() ; i++ ) {
      |                     ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1941:10: warning: unused variable 'nrows' [-Wunused-variable]
 1941 |   size_t nrows = get_num_rows();
      |          ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::tabular_output(std::ostream&, int, int, int, int, bool, char)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:2004:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 2004 |     for ( int i = 0 ; i < rts_slice.size() - 1 ; i++ ) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:2010:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 2010 |   for ( int i = 0 ; i < mzs_slice.size() ; i++ ) {
      |                     ~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:2019:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 2019 |     for ( int j = 0 ; j < out_chrom.size() - 1 ; j++ ) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1990:13: warning: unused variable 'num_mzs' [-Wunused-variable]
 1990 |   const int num_mzs = get_num_mzs();
      |             ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'virtual void msmat_scans::get_scan_interp(float, std::vector<float>&) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:2071:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 2071 |   for ( int i = 0 ; i < s1.size() ;i++ ) {
      |                     ~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'virtual void msmat_chroms::get_scan_interp(float, std::vector<float>&) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:2095:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 2095 |   for ( int i = 0 ; i < s1.size() ;i++ ) {
      |                     ~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void ttest_score_matrix::unmask_search(msmat::mz_type, msmat::rt_type, msmat::rt_type)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:2109:7: warning: unused variable 'start_rt_idx' [-Wunused-variable]
 2109 |   int start_rt_idx = this->rt_to_rtidx(start_rt);
      |       ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:2110:7: warning: unused variable 'stop_rt_idx' [-Wunused-variable]
 2110 |   int stop_rt_idx = this->rt_to_rtidx(stop_rt);
      |       ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:812:12: warning: 'int test_msmat_time_interp(msmat*)' declared 'static' but never defined [-Wunused-function]
  812 | static int test_msmat_time_interp( msmat * msmat_f );
      |            ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:813:12: warning: 'int test_msmat_sg_test(msmat*)' declared 'static' but never defined [-Wunused-function]
  813 | static int test_msmat_sg_test( msmat * msmat_fh);
      |            ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:814:12: warning: 'int test_msmat_output(msmat*, char*)' declared 'static' but never defined [-Wunused-function]
  814 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
      |            ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1740:9: warning: 'msmat* msmat_from_thevoid(const std::vector<float>&, const std::vector<float>&, std::vector<std::vector<float> >&, bool)' defined but not used [-Wunused-function]
 1740 | msmat * msmat_from_thevoid
      |         ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1713:6: warning: 'void output_bp_chrom(msmat&, char*)' defined but not used [-Wunused-function]
 1713 | void output_bp_chrom( msmat & m, char * fname  ) {
      |      ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1582:9: warning: 'msmat* test_msmat(int, char**)' defined but not used [-Wunused-function]
 1582 | msmat * test_msmat ( int argc , char ** argv ) {
      |         ^~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:48:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_base.H:69:21: warning: 'valid_fields' defined but not used [-Wunused-variable]
   69 | const static char * valid_fields[] = {
      |                     ^~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 58%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_base.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/msmat_base.cpp.o -MF CMakeFiles/MSToolkit.dir/msmat_base.cpp.o.d -o CMakeFiles/MSToolkit.dir/msmat_base.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_base.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_base.cpp:16:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_base.H:69:21: warning: 'valid_fields' defined but not used [-Wunused-variable]
   69 | const static char * valid_fields[] = {
      |                     ^~~~~~~~~~~~
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[ 56%] Building CXX object CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o -MF CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o.d -o CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o -c /builddir/build/BUILD/percolator-rel-3-05/converters/gaml_tandem1.0.cxx
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[ 60%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o -MF CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o.d -o CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:20:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'std::pair<float, float> msmat::get_transition_by_idx() const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:517:3: warning: no return statement in function returning non-void [-Wreturn-type]
  517 |   }
      |   ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'int msmat::get_idx_by_transition(std::pair<float, float>) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:519:3: warning: no return statement in function returning non-void [-Wreturn-type]
  519 |   }
      |   ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_scans::msmat_scans()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:600:15: warning: unused variable 'a' [-Wunused-variable]
  600 |           int a = 3;
      |               ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_chroms::msmat_chroms()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:703:9: warning: unused variable 'a' [-Wunused-variable]
  703 |     int a  = 3;
      |         ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp: In member function 'int msmat_header_parser::read_header(msmat*, FILE*, bool, int*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:92:14: warning: unused variable 'should_be_semi' [-Wunused-variable]
   92 |         char should_be_semi = (char)fgetc(header_fh);
      |              ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp: In member function 'void msmat_header_parser::load_strmap_from_str(std::map<std::__cxx11::basic_string<char>, float>&, const char*, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:343:22: warning: unused variable 'key_fields_len' [-Wunused-variable]
  343 |   int c1_loc, c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len;
      |                      ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:343:38: warning: unused variable 'key_last_loc' [-Wunused-variable]
  343 |   int c1_loc, c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len;
      |                                      ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:343:52: warning: unused variable 'key_data_len' [-Wunused-variable]
  343 |   int c1_loc, c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len;
      |                                                    ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:344:8: warning: unused variable 'key_len_data' [-Wunused-variable]
  344 |   char key_len_data[128], val_len_data[128];
      |        ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:344:27: warning: unused variable 'val_len_data' [-Wunused-variable]
  344 |   char key_len_data[128], val_len_data[128];
      |                           ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:367:7: warning: unused variable 'key_data_idx' [-Wunused-variable]
  367 |   int key_data_idx;
      |       ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp: In member function 'void msmat_header_parser::write_header_field_string_list(FILE*, const char*, const std::vector<std::__cxx11::basic_string<char> >&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:431:9: warning: unused variable 'num_elements' [-Wunused-variable]
  431 |     int num_elements = s.size();
      |         ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:812:12: warning: 'int test_msmat_time_interp(msmat*)' declared 'static' but never defined [-Wunused-function]
  812 | static int test_msmat_time_interp( msmat * msmat_f );
      |            ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:813:12: warning: 'int test_msmat_sg_test(msmat*)' declared 'static' but never defined [-Wunused-function]
  813 | static int test_msmat_sg_test( msmat * msmat_fh);
      |            ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:814:12: warning: 'int test_msmat_output(msmat*, char*)' declared 'static' but never defined [-Wunused-function]
  814 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
      |            ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:815:16: warning: 'msmat* test_msmat(int, char**)' declared 'static' but never defined [-Wunused-function]
  815 | static msmat * test_msmat(int argc, char ** argv);
      |                ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:818:13: warning: 'void output_bp_chrom(msmat&, char*)' declared 'static' but never defined [-Wunused-function]
  818 | static void output_bp_chrom( msmat & m , char * fname);
      |             ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:819:17: warning: 'msmat* msmat_from_fh(FILE*, sparse_level)' declared 'static' but never defined [-Wunused-function]
  819 | static msmat *  msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA );
      |                 ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:820:16: warning: 'msmat* msmat_from_thevoid(const std::vector<float>&, const std::vector<float>&, std::vector<std::vector<float> >&, bool)' declared 'static' but never defined [-Wunused-function]
  820 | static msmat * msmat_from_thevoid ( const std::vector<float> & mzs, const std::vector<float> & rts, std::vector < std::vector< float > > & chroms , bool as_scans = true );
      |                ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp: In member function 'msmat_header_parser::load_map_from_str(std::map<float, float, std::less<float>, std::allocator<std::pair<float const, float> > >&, char const*, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:314:10: warning: 'operator delete(void*, unsigned long)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  314 |   delete k;
      |          ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:306:48: note: returned from 'operator new[](unsigned long)'
  306 |   flt_map_type * k = new flt_map_type[num_items];
      |                                                ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:315:10: warning: 'operator delete(void*, unsigned long)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  315 |   delete v;
      |          ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:307:48: note: returned from 'operator new[](unsigned long)'
  307 |   flt_map_type * v = new flt_map_type[num_items];
      |                                                ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp: In member function 'msmat_header_parser::load_strmap_from_str(std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, float, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::almake[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
locator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, float> > >&, char const*, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:394:10: warning: 'operator delete(void*, unsigned long)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  394 |   delete values;
      |          ^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:389:37: note: returned from 'operator new[](unsigned long)'
  389 |   float * values = new float[val_len];
      |                                     ^
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 63%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_test.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/msmat_test.cpp.o -MF CMakeFiles/MSToolkit.dir/msmat_test.cpp.o.d -o CMakeFiles/MSToolkit.dir/msmat_test.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_test.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_test.cpp:4:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'std::pair<float, float> msmat::get_transition_by_idx() const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:517:3: warning: no return statement in function returning non-void [-Wreturn-type]
  517 |   }
      |   ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'int msmat::get_idx_by_transition(std::pair<float, float>) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:519:3: warning: no return statement in function returning non-void [-Wreturn-type]
  519 |   }
      |   ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_scans::msmat_scans()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:600:15: warning: unused variable 'a' [-Wunused-variable]
  600 |           int a = 3;
      |               ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_chroms::msmat_chroms()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:703:9: warning: unused variable 'a' [-Wunused-variable]
  703 |     int a  = 3;
      |         ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_test.cpp: In function 'int main(int, char**)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_test.cpp:13:12: warning: unused variable 'm' [-Wunused-variable]
   13 |   msmat  * m;
      |            ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:812:12: warning: 'int test_msmat_time_interp(msmat*)' declared 'static' but never defined [-Wunused-function]
  812 | static int test_msmat_time_interp( msmat * msmat_f );
      |            ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:813:12: warning: 'int test_msmat_sg_test(msmat*)' declared 'static' but never defined [-Wunused-function]
  813 | static int test_msmat_sg_test( msmat * msmat_fh);
      |            ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:814:12: warning: 'int test_msmat_output(msmat*, char*)' declared 'static' but never defined [-Wunused-function]
  814 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
      |            ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:815:16: warning: 'msmat* test_msmat(int, char**)' declared 'static' but never defined [-Wunused-function]
  815 | static msmat * test_msmat(int argc, char ** argv);
      |                ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:818:13: warning: 'void output_bp_chrom(msmat&, char*)' declared 'static' but never defined [-Wunused-function]
  818 | static void output_bp_chrom( msmat & m , char * fname);
      |             ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:819:17: warning: 'msmat* msmat_from_fh(FILE*, sparse_level)' declared 'static' but never defined [-Wunused-function]
  819 | static msmat *  msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA );
      |                 ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:820:16: warning: 'msmat* msmat_from_thevoid(const std::vector<float>&, const std::vector<float>&, std::vector<std::vector<float> >&, bool)' declared 'static' but never defined [-Wunused-function]
  820 | static msmat * msmat_from_thevoid ( const std::vector<float> & mzs, const std::vector<float> & rts, std::vector < std::vector< float > > & chroms , bool as_scans = true );
      |                ^~~~~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:48:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_base.H:69:21: warning: 'valid_fields' defined but not used [-Wunused-variable]
   69 | const static char * valid_fields[] = {
      |                     ^~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
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[ 65%] Linking CXX static library libMSToolkit.a
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/cmake -P CMakeFiles/MSToolkit.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/cmake -E cmake_link_script CMakeFiles/MSToolkit.dir/link.txt --verbose=1
/usr/bin/ar qc libMSToolkit.a CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o CMakeFiles/MSToolkit.dir/MSObject.cpp.o CMakeFiles/MSToolkit.dir/MSReader.cpp.o CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o CMakeFiles/MSToolkit.dir/MSWarper.cpp.o CMakeFiles/MSToolkit.dir/Spectrum.cpp.o CMakeFiles/MSToolkit.dir/crawutils.cpp.o CMakeFiles/MSToolkit.dir/msmat.cpp.o CMakeFiles/MSToolkit.dir/msmat_base.cpp.o CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o CMakeFiles/MSToolkit.dir/msmat_test.cpp.o
/usr/bin/ranlib libMSToolkit.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 65%] Built target MSToolkit
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
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/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o -MF CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o.d -o CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o -c /builddir/build/BUILD/percolator-rel-3-05/converters/tandem2011.12.01.1.cxx
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/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/Reader.cpp.o -MF CMakeFiles/converters.dir/Reader.cpp.o.d -o CMakeFiles/converters.dir/Reader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/Reader.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/Reader.cpp: In member function 'Reader::translateFileToXML(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, unsigned int, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/Reader.cpp:327:32: warning: 'tcd' may be used uninitialized [-Wmaybe-uninitialized]
  327 |         tmpDirs[lineNumber_par]=tcd;
/builddir/build/BUILD/percolator-rel-3-05/src/converters/Reader.cpp:302:22: note: 'tcd' was declared here
  302 |               char * tcd;
      |                      ^~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
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/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/SqtReader.cpp.o -MF CMakeFiles/converters.dir/SqtReader.cpp.o.d -o CMakeFiles/converters.dir/SqtReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/SqtReader.cpp
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[ 70%] Building CXX object CMakeFiles/converters.dir/MzidentmlReader.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/MzidentmlReader.cpp.o -MF CMakeFiles/converters.dir/MzidentmlReader.cpp.o.d -o CMakeFiles/converters.dir/MzidentmlReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MzidentmlReader.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MzidentmlReader.cpp: In member function 'virtual void MzidentmlReader::getMaxMinCharge(const std::string&, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MzidentmlReader.cpp:86:30: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=]
   86 |   } catch (ifstream::failure e) {
      |                              ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MzidentmlReader.cpp:94:24: warning: catching polymorphic type 'class MyException' by value [-Wcatch-value=]
   94 |   } catch (MyException e) {
      |                        ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MzidentmlReader.cpp:97:27: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=]
   97 |   } catch (std::exception e) {
      |                           ^
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[ 72%] Building CXX object CMakeFiles/converters.dir/SequestReader.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/SequestReader.cpp.o -MF CMakeFiles/converters.dir/SequestReader.cpp.o.d -o CMakeFiles/converters.dir/SequestReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/SequestReader.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/SequestReader.cpp: In member function 'virtual void SequestReader::createPSM(const mzIdentML_ns::SpectrumIdentificationItemType&, percolatorInNs::fragSpectrumScan::experimentalMass_type, bool, unsigned int, boost::shared_ptr<FragSpectrumScanDatabase>, const std::string&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/SequestReader.cpp:169:12: warning: unused variable 'PI' [-Wunused-variable]
  169 |     double PI = boost::lexical_cast<double>(item.calculatedPI().get());
      |            ^~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/SequestReader.cpp:174:14: warning: unused variable 'peptide_length' [-Wunused-variable]
  174 |     unsigned peptide_length = peptideLength(peptideSeqWithFlanks);
      |              ^~~~~~~~~~~~~~
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[ 74%] Building CXX object CMakeFiles/converters.dir/MsgfplusReader.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/MsgfplusReader.cpp.o -MF CMakeFiles/converters.dir/MsgfplusReader.cpp.o.d -o CMakeFiles/converters.dir/MsgfplusReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MsgfplusReader.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MsgfplusReader.cpp: In member function 'virtual void MsgfplusReader::createPSM(const mzIdentML_ns::SpectrumIdentificationItemType&, percolatorInNs::fragSpectrumScan::experimentalMass_type, bool, unsigned int, boost::shared_ptr<FragSpectrumScanDatabase>, const std::string&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MsgfplusReader.cpp:333:27: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
  333 |                           else StdevErrorTop7 = boost::lexical_cast<double>(up.value().get().c_str()); break;
      |                           ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MsgfplusReader.cpp:333:104: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
  333 |                           else StdevErrorTop7 = boost::lexical_cast<double>(up.value().get().c_str()); break;
      |                                                                                                        ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MsgfplusReader.cpp:272:14: warning: unused variable 'peptide_length' [-Wunused-variable]
  272 |     unsigned peptide_length = peptideLength(peptideSeqWithFlanks);
      |              ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MsgfplusReader.cpp:291:12: warning: variable 'SpecEValue' set but not used [-Wunused-but-set-variable]
  291 |     double SpecEValue = 0.0;
      |            ^~~~~~~~~~
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/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o -MF CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o.d -o CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/FragSpectrumScanDatabase.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/FragSpectrumScanDatabase.cpp: In member function 'std::string FragSpectrumScanDatabase::decoratePeptide(const percolatorInNs::peptideType&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/FragSpectrumScanDatabase.cpp:80:19: warning: comparison of integer expressions of different signedness: 'const int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   80 |     if (it->first <= peptideSeq.length()) {
      |         ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
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/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/TandemReader.cpp.o -MF CMakeFiles/converters.dir/TandemReader.cpp.o.d -o CMakeFiles/converters.dir/TandemReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/TandemReader.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/TandemReader.cpp: In member function 'virtual void TandemReader::getMaxMinCharge(const std::string&, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/TandemReader.cpp:274:24: warning: catching polymorphic type 'class MyException' by value [-Wcatch-value=]
  274 |   } catch (MyException e) {
      |                        ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/TandemReader.cpp:277:27: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=]
  277 |   } catch (std::exception e) {
      |                           ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/TandemReader.cpp: In member function 'void TandemReader::createPSM(const tandem_ns::peptide::domain_type&, double, unsigned int, double, double, bool, boost::shared_ptr<FragSpectrumScanDatabase>, const peptideProteinMapType&, const std::string&, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/TandemReader.cpp:497:29: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  497 |     f_seq.push_back( charge == c ? 1.0 : 0.0);
      |                      ~~~~~~~^~~~
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/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o -MF CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o.d -o CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/FragSpectrumScanDatabaseTokyodb.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/FragSpectrumScanDatabaseTokyodb.cpp: In member function 'virtual void FragSpectrumScanDatabaseTokyoDB::putFSS(percolatorInNs::fragSpectrumScan&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/FragSpectrumScanDatabaseTokyodb.cpp:165:10: warning: unused variable 'valueSize' [-Wunused-variable]
  165 |   size_t valueSize(buf.size ());
      |          ^~~~~~~~~
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/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/Interface.cpp.o -MF CMakeFiles/converters.dir/Interface.cpp.o.d -o CMakeFiles/converters.dir/Interface.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/Interface.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/Interface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/Interface.h: In constructor 'Interface::Interface()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/Interface.h:50:14: warning: 'Interface::xmlOutput' will be initialized after [-Wreorder]
   50 |         bool xmlOutput;
      |              ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/Interface.h:47:21: warning:   'std::string Interface::outputFN' [-Wreorder]
   47 |         std::string outputFN;
      |                     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/Interface.cpp:21:1: warning:   when initialized here [-Wreorder]
   21 | Interface::Interface() : xmlOutput(false), outputFN("") { }
      | ^~~~~~~~~
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/usr/bin/ar qc libconverters.a CMakeFiles/converters.dir/mzIdentML1.1.0.cxx.o CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o CMakeFiles/converters.dir/Reader.cpp.o CMakeFiles/converters.dir/SqtReader.cpp.o CMakeFiles/converters.dir/MzidentmlReader.cpp.o CMakeFiles/converters.dir/SequestReader.cpp.o CMakeFiles/converters.dir/MsgfplusReader.cpp.o CMakeFiles/converters.dir/TandemReader.cpp.o CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o CMakeFiles/converters.dir/Interface.cpp.o CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o
/usr/bin/ranlib libconverters.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 89%] Built target converters
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make  -f CMakeFiles/msgf2pin.dir/build.make CMakeFiles/msgf2pin.dir/depend
/usr/bin/make  -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/sqt2pin.dir/DependInfo.cmake --color=
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/msgf2pin.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 90%] Building CXX object CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o -MF CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o.d -o CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/Msgfplus2Pin.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 92%] Building CXX object CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o -MF CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o.d -o CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/Sqt2Pin.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 96%] Linking CXX executable sqt2pin
/usr/bin/cmake -E cmake_link_script CMakeFiles/sqt2pin.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -rdynamic CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o -o sqt2pin   -L/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src  libconverters.a libperclibrary_part.a MSToolkit/libMSToolkit.a -lxerces-c /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_atomic.a /usr/lib64/libboost_system.a -ltokyocabinet -lbz2 -lz -lsqlite3 MSToolkit/RAMP/libRAMP.a -ldl 
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
In function 'strchr',
    inlined from 'readPeaks' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1599:35:
/usr/include/string.h:241:27: warning: '__builtin_strchr' reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
  241 |   return __builtin_strchr (__s, __c);
      |                           ^
In function 'strchr',
    inlined from 'readPeaks' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1613:35:
/usr/include/string.h:241:27: warning: '__builtin_strchr' reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
  241 |   return __builtin_strchr (__s, __c);
      |                           ^
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 96%] Built target sqt2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make  -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/tandem2pin.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 98%] Building CXX object CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o -MF CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o.d -o CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/Tandem2Pin.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 94%] Linking CXX executable msgf2pin
/usr/bin/cmake -E cmake_link_script CMakeFiles/msgf2pin.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -rdynamic CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o -o msgf2pin   -L/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src  libconverters.a libperclibrary_part.a MSToolkit/libMSToolkit.a -lxerces-c /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_atomic.a /usr/lib64/libboost_system.a -ltokyocabinet -lbz2 -lz -lsqlite3 MSToolkit/RAMP/libRAMP.a -ldl 
In function 'strchr',
    inlined from 'readPeaks' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1599:35:
/usr/include/string.h:241:27: warning: '__builtin_strchr' reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
  241 |   return __builtin_strchr (__s, __c);
      |                           ^
In function 'strchr',
    inlined from 'readPeaks' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1613:35:
/usr/include/string.h:241:27: warning: '__builtin_strchr' reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
  241 |   return __builtin_strchr (__s, __c);
      |                           ^
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[100%] Built target msgf2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[100%] Linking CXX executable tandem2pin
/usr/bin/cmake -E cmake_link_script CMakeFiles/tandem2pin.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -rdynamic CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o -o tandem2pin   -L/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src  libconverters.a libperclibrary_part.a MSToolkit/libMSToolkit.a -lxerces-c /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_atomic.a /usr/lib64/libboost_system.a -ltokyocabinet -lbz2 -lz -lsqlite3 MSToolkit/RAMP/libRAMP.a -ldl 
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
In function 'strchr',
    inlined from 'readPeaks' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1599:35:
/usr/include/string.h:241:27: warning: '__builtin_strchr' reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
  241 |   return __builtin_strchr (__s, __c);
      |                           ^
In function 'strchr',
    inlined from 'readPeaks' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1613:35:
/usr/include/string.h:241:27: warning: '__builtin_strchr' reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
  241 |   return __builtin_strchr (__s, __c);
      |                           ^
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[100%] Built target tandem2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles 0
+ popd
~/build/BUILD/percolator-rel-3-05
+ mkdir -p elude
+ pushd elude
~/build/BUILD/percolator-rel-3-05/elude ~/build/BUILD/percolator-rel-3-05
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ /usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -Wno-dev -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE=TRUE -DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_PREFIX_PATH:STRING=/usr -DBoost_USE_STATIC_LIBS:BOOL=OFF -DCMAKE_USE_RELATIVE_PATHS:BOOL=ON '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc' -DTARGET_ARCH=x86_64 ../src/elude_tool
-- The C compiler identification is GNU 12.2.1
-- The CXX compiler identification is GNU 12.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
-- 
-- -------------------------------------------------------------------------------
-- Building ELUDE:
-- change a configuration variable with: cmake -D<Variable>=<Value>
-- CMAKE_INSTALL_PREFIX = /usr
-- CMAKE_BUILD_TYPE = Release
-- PERCOLATOR_SOURCE_DIR = /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../..
-- CMAKE_PREFIX_PATH = /usr
-- GOOGLE_TEST = 
-- GOOGLE_TEST_PATH = 
-- TARGET_ARCH = x86_64
-- PROFILING = 
-- -------------------------------------------------------------------------------
-- 
-- Architecture: 
-- Found Boost: /usr/lib64/cmake/Boost-1.78.0/BoostConfig.cmake (found version "1.78.0")  
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    CMAKE_Fortran_FLAGS_RELEASE
    CMAKE_INSTALL_DO_STRIP
    CMAKE_SKIP_INSTALL_RPATH
    CMAKE_USE_RELATIVE_PATHS
    INCLUDE_INSTALL_DIR
    LIB_INSTALL_DIR
    LIB_SUFFIX
    SHARE_INSTALL_PREFIX
    SYSCONF_INSTALL_DIR


-- Build files have been written to: /builddir/build/BUILD/percolator-rel-3-05/elude
+ /usr/bin/make -O -j2 V=1 VERBOSE=1
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool -B/builddir/build/BUILD/percolator-rel-3-05/elude --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles /builddir/build/BUILD/percolator-rel-3-05/elude//CMakeFiles/progress.marks
/usr/bin/make  -f CMakeFiles/Makefile2 all
/usr/bin/make  -f CMakeFiles/eludelibrary.dir/build.make CMakeFiles/eludelibrary.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
cd /builddir/build/BUILD/percolator-rel-3-05/elude && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles/eludelibrary.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/usr/bin/make  -f CMakeFiles/eludelibrary.dir/build.make CMakeFiles/eludelibrary.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[  8%] Building CXX object CMakeFiles/eludelibrary.dir/RetentionFeatures.cpp.o
/usr/bin/g++  -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/RetentionFeatures.cpp.o -MF CMakeFiles/eludelibrary.dir/RetentionFeatures.cpp.o.d -o CMakeFiles/eludelibrary.dir/RetentionFeatures.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionFeatures.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionFeatures.cpp: In static member function 'static double RetentionFeatures::IndexN(const std::string&, const std::map<std::__cxx11::basic_string<char>, double>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionFeatures.cpp:304:21: warning: unused variable 'len' [-Wunused-variable]
  304 |   int end_position, len = peptide.size();
      |                     ^~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[ 13%] Building CXX object CMakeFiles/eludelibrary.dir/EludeMain.cpp.o
/usr/bin/g++  -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/EludeMain.cpp.o -MF CMakeFiles/eludelibrary.dir/EludeMain.cpp.o.d -o CMakeFiles/eludelibrary.dir/EludeMain.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeMain.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[ 17%] Building CXX object CMakeFiles/eludelibrary.dir/LibSVRModel.cpp.o
/usr/bin/g++  -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/LibSVRModel.cpp.o -MF CMakeFiles/eludelibrary.dir/LibSVRModel.cpp.o.d -o CMakeFiles/eludelibrary.dir/LibSVRModel.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:27:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h: In member function 'bool LibSVRModel::IsModelNull() const':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h:57:65: warning: second operand of conditional expression has no effect [-Wunused-value]
   57 |    inline bool IsModelNull() const { svr_ == NULL ? true : false; }
      |                                                                 ^
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h:57:65: warning: third operand of conditional expression has no effect [-Wunused-value]
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h:57:67: warning: no return statement in function returning non-void [-Wreturn-type]
   57 |    inline bool IsModelNull() const { svr_ == NULL ? true : false; }
      |                                                                   ^
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'virtual int LibSVRModel::LoadModel(FILE*)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:284:1: warning: control reaches end of non-void function [-Wreturn-type]
  284 | }
      | ^
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateLinearModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:205:21: warning: 'best_e' may be used uninitialized [-Wmaybe-uninitialized]
  205 |   svr_parameters_.p = best_e;
      |   ~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:182:18: note: 'best_e' was declared here
  182 |   double best_c, best_e;
      |                  ^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:204:21: warning: 'best_c' may be used uninitialized [-Wmaybe-uninitialized]
  204 |   svr_parameters_.C = best_c;
      |   ~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:182:10: note: 'best_c' was declared here
  182 |   double best_c, best_e;
      |          ^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateRBFModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:242:25: warning: 'best_g' may be used uninitialized [-Wmaybe-uninitialized]
  242 |   svr_parameters_.gamma = best_g;
      |   ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:213:26: note: 'best_g' was declared here
  213 |   double best_c, best_e, best_g;
      |                          ^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:241:21: warning: 'best_e' may be used uninitialized [-Wmaybe-uninitialized]
  241 |   svr_parameters_.p = best_e;
      |   ~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:213:18: note: 'best_e' was declared here
  213 |   double best_c, best_e, best_g;
      |                  ^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:240:21: warning: 'best_c' may be used uninitialized [-Wmaybe-uninitialized]
  240 |   svr_parameters_.C = best_c;
      |   ~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:213:10: note: 'best_c' was declared here
  213 |   double best_c, best_e, best_g;
      |          ^~~~~~
In member function 'LibSVRModel::CalibrateRBFModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)',
    inlined from 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)' at /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:255:29:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:242:25: warning: 'best_g' may be used uninitialized [-Wmaybe-uninitialized]
  242 |   svr_parameters_.gamma = best_g;
      |   ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:213:26: note: 'best_g' was declared here
  213 |   double best_c, best_e, best_g;
      |                          ^~~~~~
In member function 'LibSVRModel::CalibrateRBFModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)',
    inlined from 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)' at /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:255:29:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:241:21: warning: 'best_e' may be used uninitialized [-Wmaybe-uninitialized]
  241 |   svr_parameters_.p = best_e;
      |   ~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:213:18: note: 'best_e' was declared here
  213 |   double best_c, best_e, best_g;
      |                  ^~~~~~
In member function 'LibSVRModel::CalibrateRBFModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)',
    inlined from 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)' at /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:255:29:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:240:21: warning: 'best_c' may be used uninitialized [-Wmaybe-uninitialized]
  240 |   svr_parameters_.C = best_c;
      |   ~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:213:10: note: 'best_c' was declared here
  213 |   double best_c, best_e, best_g;
      |          ^~~~~~
In member function 'LibSVRModel::CalibrateLinearModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)',
    inlined from 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)' at /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:253:32:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:205:21: warning: 'best_e' may be used uninitialized [-Wmaybe-uninitialized]
  205 |   svr_parameters_.p = best_e;
      |   ~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:182:18: note: 'best_e' was declared here
  182 |   double best_c, best_e;
      |                  ^~~~~~
In member function 'LibSVRModel::CalibrateLinearModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)',
    inlined from 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)' at /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:253:32:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:204:21: warning: 'best_c' may be used uninitialized [-Wmaybe-uninitialized]
  204 |   svr_parameters_.C = best_c;
      |   ~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:182:10: note: 'best_c' was declared here
  182 |   double best_c, best_e;
      |          ^~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[ 21%] Building CXX object CMakeFiles/eludelibrary.dir/LibsvmWrapper.cpp.o
/usr/bin/g++  -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/LibsvmWrapper.cpp.o -MF CMakeFiles/eludelibrary.dir/LibsvmWrapper.cpp.o.d -o CMakeFiles/eludelibrary.dir/LibsvmWrapper.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibsvmWrapper.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibsvmWrapper.cpp: In function 'svm_model* libsvm_wrapper::LoadModel(FILE*)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibsvmWrapper.cpp:172:7: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
  172 |   int ret;
      |       ^~~
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/usr/bin/g++  -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/DataManager.cpp.o -MF CMakeFiles/eludelibrary.dir/DataManager.cpp.o.d -o CMakeFiles/eludelibrary.dir/DataManager.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/DataManager.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/DataManager.cpp: In static member function 'static std::vector<std::pair<PSMDescription*, std::__cxx11::basic_string<char> > > DataManager::RemoveInSourceFragments(const Enzyme*, const double&, const std::map<std::__cxx11::basic_string<char>, double>&, bool, std::vector<PSMDescription*>&, std::vector<PSMDescription*>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/DataManager.cpp:334:50: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<PSMDescription*>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  334 |     if (!remove_from_test && (initial_train_size != train_psms.size())) {
      |                               ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/DataManager.cpp: In static member function 'static std::vector<PSMDescription*> DataManager::RemoveNonEnzymatic(const Enzyme*, std::vector<PSMDescription*>&, const std::string&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/DataManager.cpp:354:7: warning: unused variable 'initial_size' [-Wunused-variable]
  354 |   int initial_size = psms.size();
      |       ^~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[ 26%] Building CXX object CMakeFiles/eludelibrary.dir/RetentionModel.cpp.o
/usr/bin/g++  -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/RetentionModel.cpp.o -MF CMakeFiles/eludelibrary.dir/RetentionModel.cpp.o.d -o CMakeFiles/eludelibrary.dir/RetentionModel.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:17:1: warning: "/*" within comment [-Wcomment]
   17 | /*
      |  
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:27:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h: In member function 'bool LibSVRModel::IsModelNull() const':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h:57:65: warning: second operand of conditional expression has no effect [-Wunused-value]
   57 |    inline bool IsModelNull() const { svr_ == NULL ? true : false; }
      |                                                                 ^
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h:57:65: warning: third operand of conditional expression has no effect [-Wunused-value]
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h:57:67: warning: no return statement in function returning non-void [-Wreturn-type]
   57 |    inline bool IsModelNull() const { svr_ == NULL ? true : false; }
      |                                                                   ^
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:24:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.h: In constructor 'RetentionModel::RetentionModel(Normalizer*)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.h:99:16: warning: 'RetentionModel::the_normalizer_' will be initialized after [-Wreorder]
   99 |    Normalizer *the_normalizer_;
      |                ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.h:95:14: warning:   'SVRModel* RetentionModel::svr_model_' [-Wreorder]
   95 |    SVRModel *svr_model_;
      |              ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:30:1: warning:   when initialized here [-Wreorder]
   30 | RetentionModel::RetentionModel(Normalizer *norm) : the_normalizer_(norm),
      | ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp: In destructor 'RetentionModel::~RetentionModel()':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:36:5: warning: deleting object of abstract class type 'SVRModel' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
   36 |     delete svr_model_;
      |     ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp: In member function 'void RetentionModel::PrintSub()':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:62:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   62 |   for(int i = 0; i < vsub_.size(); ++i)
      |                  ~~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp: In member function 'int RetentionModel::TrainRetentionModel(const std::set<std::__cxx11::basic_string<char> >&, const std::map<std::__cxx11::basic_string<char>, double>&, bool, std::vector<PSMDescription*>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:187:5: warning: deleting object of abstract class type 'SVRModel' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
  187 |     delete svr_model_;
      |     ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp: In member function 'int RetentionModel::SaveModelToFile(const std::string&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:291:20: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  291 |   if (vsub_.size() !=  number_features) {
      |       ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp: In member function 'int RetentionModel::LoadModelFromFile(const std::string&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:356:5: warning: deleting object of abstract class type 'SVRModel' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
  356 |     delete svr_model_;
      |     ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:363:24: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
  363 |   int number_features, ret;
      |                        ^~~
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/usr/bin/g++  -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/LTSRegression.cpp.o -MF CMakeFiles/eludelibrary.dir/LTSRegression.cpp.o.d -o CMakeFiles/eludelibrary.dir/LTSRegression.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::setData(std::vector<double>&, std::vector<double>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp:48:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   48 |   for (int i = 0; i < x.size(); ++i) {
      |                   ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::fillResiduals(std::pair<double, double>)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp:84:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<dataPoint>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   84 |   for (int i = 0; i < data.size(); ++i) {
      |                   ~~^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::runLTS()':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp:168:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  168 |         for (int i = 1; i < Q.size(); ++i)
      |                         ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp:177:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<dataPoint> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  177 |   for (int j = 0; j < best10Subsets.size(); ++j) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::printVector(std::vector<dataPoint>)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp:209:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<dataPoint>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  209 |   for (int i = 0; i < v.size(); ++i) {
      |                   ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::printDataPoints()':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp:220:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<dataPoint>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  220 |   for (int i = h; i < data.size(); ++i) {
      |                   ~~^~~~~~~~~~~~~
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/usr/bin/g++  -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/EludeCaller.cpp.o -MF CMakeFiles/eludelibrary.dir/EludeCaller.cpp.o.d -o CMakeFiles/eludelibrary.dir/EludeCaller.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:30:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h: In constructor 'EludeCaller::EludeCaller()':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:167:9: warning: 'EludeCaller::remove_non_enzymatic_' will be initialized after [-Wreorder]
  167 |    bool remove_non_enzymatic_;
      |         ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:143:9: warning:   'bool EludeCaller::context_format_' [-Wreorder]
  143 |    bool context_format_;
      |         ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:44:1: warning:   when initialized here [-Wreorder]
   44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
      | ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:189:20: warning: 'EludeCaller::rt_model_' will be initialized after [-Wreorder]
  189 |    RetentionModel *rt_model_;
      |                    ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:173:9: warning:   'bool EludeCaller::ignore_ptms_' [-Wreorder]
  173 |    bool ignore_ptms_;
      |         ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:44:1: warning:   when initialized here [-Wreorder]
   44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
      | ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:196:9: warning: 'EludeCaller::supress_print_' will be initialized after [-Wreorder]
  196 |    bool supress_print_;
      |         ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:175:9: warning:   'bool EludeCaller::only_hydrophobicity_index_' [-Wreorder]
  175 |    bool only_hydrophobicity_index_;
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:44:1: warning:   when initialized here [-Wreorder]
   44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
      | ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In member function 'int EludeCaller::AddModelLibrary() const':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:519:20: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
  519 |       while (found != string::npos) {
      |              ~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In member function 'int EludeCaller::Run()':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:639:9: warning: unused variable 'ret' [-Wunused-variable]
  639 |     int ret = 1;
      |         ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In static member function 'static double EludeCaller::ComputeRankCorrelation(std::vector<PSMDescription*>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:940:10: warning: unused variable 'corr' [-Wunused-variable]
  940 |   double corr = 0.0, d = 0.0, avg_rank, rank_p;
      |          ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In static member function 'static std::string EludeCaller::GetFileName(const std::string&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:1026:39: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
 1026 |   if ((pos1 = path.find_last_of("/")) == string::npos) {
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:1027:41: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
 1027 |     if ((pos1 = path.find_last_of("\\"))== string::npos) {
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:1032:44: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
 1032 |   if ((pos2 = file_name.find_last_of(".")) != string::npos) {
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
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/usr/bin/g++  -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp.o -MF CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp.o.d -o CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp:21:
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h: In constructor 'PSMDescriptionDOC::PSMDescriptionDOC()':
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:42: warning: 'PSMDescriptionDOC::retentionTime_' will be initialized after [-Wreorder]
   92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
      |                                          ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:26: warning:   'double PSMDescriptionDOC::predictedTime_' [-Wreorder]
   92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
      |                          ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp:26:1: warning:   when initialized here [-Wreorder]
   26 | PSMDescriptionDOC::PSMDescriptionDOC() :
      | ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h: In constructor 'PSMDescriptionDOC::PSMDescriptionDOC(std::string, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:42: warning: 'PSMDescriptionDOC::retentionTime_' will be initialized after [-Wreorder]
   92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
      |                                          ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:26: warning:   'double PSMDescriptionDOC::predictedTime_' [-Wreorder]
   92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
      |                          ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp:30:1: warning:   when initialized here [-Wreorder]
   30 | PSMDescriptionDOC::PSMDescriptionDOC(const string pep, const double retTime) :
      | ^~~~~~~~~~~~~~~~~
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/usr/bin/ranlib libeludelibrary.a
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[ 91%] Built target eludelibrary
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
cd /builddir/build/BUILD/percolator-rel-3-05/elude && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles/elude.dir/DependInfo.cmake --color=
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[ 95%] Building CXX object CMakeFiles/elude.dir/EludeCaller.cpp.o
/usr/bin/g++  -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/elude.dir/EludeCaller.cpp.o -MF CMakeFiles/elude.dir/EludeCaller.cpp.o.d -o CMakeFiles/elude.dir/EludeCaller.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:30:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h: In constructor 'EludeCaller::EludeCaller()':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:167:9: warning: 'EludeCaller::remove_non_enzymatic_' will be initialized after [-Wreorder]
  167 |    bool remove_non_enzymatic_;
      |         ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:143:9: warning:   'bool EludeCaller::context_format_' [-Wreorder]
  143 |    bool context_format_;
      |         ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:44:1: warning:   when initialized here [-Wreorder]
   44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
      | ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:189:20: warning: 'EludeCaller::rt_model_' will be initialized after [-Wreorder]
  189 |    RetentionModel *rt_model_;
      |                    ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:173:9: warning:   'bool EludeCaller::ignore_ptms_' [-Wreorder]
  173 |    bool ignore_ptms_;
      |         ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:44:1: warning:   when initialized here [-Wreorder]
   44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
      | ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:196:9: warning: 'EludeCaller::supress_print_' will be initialized after [-Wreorder]
  196 |    bool supress_print_;
      |         ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:175:9: warning:   'bool EludeCaller::only_hydrophobicity_index_' [-Wreorder]
  175 |    bool only_hydrophobicity_index_;
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:44:1: warning:   when initialized here [-Wreorder]
   44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
      | ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In member function 'int EludeCaller::AddModelLibrary() const':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:519:20: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
  519 |       while (found != string::npos) {
      |              ~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In member function 'int EludeCaller::Run()':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:639:9: warning: unused variable 'ret' [-Wunused-variable]
  639 |     int ret = 1;
      |         ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In static member function 'static double EludeCaller::ComputeRankCorrelation(std::vector<PSMDescription*>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:940:10: warning: unused variable 'corr' [-Wunused-variable]
  940 |   double corr = 0.0, d = 0.0, avg_rank, rank_p;
      |          ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In static member function 'static std::string EludeCaller::GetFileName(const std::string&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:1026:39: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
 1026 |   if ((pos1 = path.find_last_of("/")) == string::npos) {
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:1027:41: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
 1027 |     if ((pos1 = path.find_last_of("\\"))== string::npos) {
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:1032:44: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
 1032 |   if ((pos2 = file_name.find_last_of(".")) != string::npos) {
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[100%] Linking CXX executable elude
/usr/bin/cmake -E cmake_link_script CMakeFiles/elude.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -rdynamic CMakeFiles/elude.dir/EludeCaller.cpp.o -o elude   -L/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src  libeludelibrary.a 
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[100%] Built target elude
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles 0
+ popd
~/build/BUILD/percolator-rel-3-05
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.zNPX4X
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64
++ dirname /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd percolator-rel-3-05
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64 'INSTALL=/usr/bin/install -p' -C percolator
make: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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[100%] Built target qvality
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/percolator/CMakeFiles 0
/usr/bin/make  -f CMakeFiles/Makefile2 preinstall
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[1]: Nothing to be done for 'preinstall'.
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/xml/percolator/xml-pin-1-3/percolator_in.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/xml/percolator/xml-pout-1-5/percolator_out.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/percolator
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/qvality
make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64 'INSTALL=/usr/bin/install -p' -C converters
make: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-05/src/converters -B/builddir/build/BUILD/percolator-rel-3-05/converters --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles /builddir/build/BUILD/percolator-rel-3-05/converters//CMakeFiles/progress.marks
/usr/bin/make  -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make  -f CMakeFiles/perclibrary_part.dir/build.make CMakeFiles/perclibrary_part.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/perclibrary_part.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make  -f CMakeFiles/perclibrary_part.dir/build.make CMakeFiles/perclibrary_part.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Nothing to be done for 'CMakeFiles/perclibrary_part.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 23%] Built target perclibrary_part
/usr/bin/make  -f CMakeFiles/generate_perc_xsdfiles.dir/build.make CMakeFiles/generate_perc_xsdfiles.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/generate_perc_xsdfiles.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make  -f CMakeFiles/generate_perc_xsdfiles.dir/build.make CMakeFiles/generate_perc_xsdfiles.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Nothing to be done for 'CMakeFiles/generate_perc_xsdfiles.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 27%] Built target generate_perc_xsdfiles
/usr/bin/make  -f CMakeFiles/converters.dir/build.make CMakeFiles/converters.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/converters.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make  -f CMakeFiles/converters.dir/build.make CMakeFiles/converters.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Nothing to be done for 'CMakeFiles/converters.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 56%] Built target converters
/usr/bin/make  -f MSToolkit/RAMP/CMakeFiles/RAMP.dir/build.make MSToolkit/RAMP/CMakeFiles/RAMP.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit/RAMP/CMakeFiles/RAMP.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make  -f MSToolkit/RAMP/CMakeFiles/RAMP.dir/build.make MSToolkit/RAMP/CMakeFiles/RAMP.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Nothing to be done for 'MSToolkit/RAMP/CMakeFiles/RAMP.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 61%] Built target RAMP
/usr/bin/make  -f MSToolkit/CMakeFiles/MSToolkit.dir/build.make MSToolkit/CMakeFiles/MSToolkit.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit/CMakeFiles/MSToolkit.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make  -f MSToolkit/CMakeFiles/MSToolkit.dir/build.make MSToolkit/CMakeFiles/MSToolkit.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Nothing to be done for 'MSToolkit/CMakeFiles/MSToolkit.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 89%] Built target MSToolkit
/usr/bin/make  -f CMakeFiles/msgf2pin.dir/build.make CMakeFiles/msgf2pin.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/msgf2pin.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make  -f CMakeFiles/msgf2pin.dir/build.make CMakeFiles/msgf2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Nothing to be done for 'CMakeFiles/msgf2pin.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 92%] Built target msgf2pin
/usr/bin/make  -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/sqt2pin.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make  -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Nothing to be done for 'CMakeFiles/sqt2pin.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 96%] Built target sqt2pin
/usr/bin/make  -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/tandem2pin.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make  -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Nothing to be done for 'CMakeFiles/tandem2pin.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[100%] Built target tandem2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles 0
/usr/bin/make  -f CMakeFiles/Makefile2 preinstall
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[1]: Nothing to be done for 'preinstall'.
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/msgf2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/sqt2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/tandem2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/percolator/xml-1-1/mzIdentML1.1.0.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/percolator/xml-2011.12.01.1/gaml_tandem1.0.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/percolator/xml-2011.12.01.1/tandem2011.12.01.1.xsd
make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64 'INSTALL=/usr/bin/install -p' -C elude
make: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool -B/builddir/build/BUILD/percolator-rel-3-05/elude --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles /builddir/build/BUILD/percolator-rel-3-05/elude//CMakeFiles/progress.marks
/usr/bin/make  -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/usr/bin/make  -f CMakeFiles/eludelibrary.dir/build.make CMakeFiles/eludelibrary.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
cd /builddir/build/BUILD/percolator-rel-3-05/elude && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles/eludelibrary.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/usr/bin/make  -f CMakeFiles/eludelibrary.dir/build.make CMakeFiles/eludelibrary.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
make[2]: Nothing to be done for 'CMakeFiles/eludelibrary.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[ 91%] Built target eludelibrary
/usr/bin/make  -f CMakeFiles/elude.dir/build.make CMakeFiles/elude.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
cd /builddir/build/BUILD/percolator-rel-3-05/elude && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles/elude.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/usr/bin/make  -f CMakeFiles/elude.dir/build.make CMakeFiles/elude.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
make[2]: Nothing to be done for 'CMakeFiles/elude.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[100%] Built target elude
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles 0
/usr/bin/make  -f CMakeFiles/Makefile2 preinstall
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
make[1]: Nothing to be done for 'preinstall'.
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/elude
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/yeast_60.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/yeast_40.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/yeast_20.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/tfa.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Luna_90.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Luna_60.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Luna_240.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Luna_180.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Luna_120.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Jupiter_90.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Jupiter_60.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Jupiter_240.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Jupiter_180.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Jupiter_120.model
make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
+ mkdir -p /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/lib64/percolator
++ find . -type f '(' -name '*.a' ')'
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./elude/libeludelibrary.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/libconverters.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/libperclibrary_part.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/MSToolkit/libMSToolkit.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/MSToolkit/RAMP/libRAMP.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./fido/libfido.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/libperclibrary.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/picked_protein/libpicked_protein.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/fido/libfido.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/blas/libblas.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/lib64/percolator
+ /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 3.05-10.fc38 --unique-debug-suffix -3.05-10.fc38.x86_64 --unique-debug-src-base percolator-3.05-10.fc38.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/percolator-rel-3-05
extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/elude
extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/msgf2pin
extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/percolator
extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/qvality
extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/sqt2pin
extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/tandem2pin
original debug info size: 82912kB, size after compression: 66996kB
/usr/bin/sepdebugcrcfix: Updated 6 CRC32s, 0 CRC32s did match.
6052 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.x86_64/src/serializer.hxx is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.x86_64/src/serializer.cxx is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.x86_64/src/parser.hxx is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.x86_64/src/parser.cxx is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.x86_64/percolator/src/Globals.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.x86_64/elude/Globals.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.x86_64/converters/Globals.h is executable but has no shebang, removing executable bit
+ /usr/lib/rpm/brp-remove-la-files
+ /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0
+ /usr/lib/rpm/redhat/brp-python-hardlink
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.a6QuvY
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd percolator-rel-3-05
+ mkdir -p test
+ cd test
+ ../converters/sqt2pin -o pin.tab ../yeast-01.sqt ../yeast-01.shuffled.sqt

Pin-converter version 3.05.0, Build Date Jul 22 2022 00:00:00
Copyright (c) 2013 Lukas Käll. All rights reserved.
Written by Lukas Käll (lukas.kall@scilifelab.se) in the
School of Biotechnology at KTH - Royal Institute of Technology, Stockholm.
Issued command:
../converters/sqt2pin -o pin.tab ../yeast-01.sqt ../yeast-01.shuffled.sqt
on 036323bce7fe4868a3584addca4b1207
Reading ../yeast-01.sqt
Reading ../yeast-01.shuffled.sqt
+ ../percolator/src/percolator -X pout.xml pin.tab
Percolator version 3.05.0, Build Date Jul 22 2022 00:00:00
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
../percolator/src/percolator -X pout.xml pin.tab
Started Sun Nov 13 06:49:33 2022
 on 036323bce7fe4868a3584addca4b1207
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile pin.tab
Features:
lnrSp deltLCn deltCn Xcorr Sp IonFrac Mass PepLen Charge1 Charge2 Charge3 enzN enzC enzInt lnNumSP dM absdM 
Found 139410 PSMs
Separate target and decoy search inputs detected, using mix-max method.
Train/test set contains 69705 positives and 69705 negatives, size ratio=1 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Found 7004 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.700987 cpu seconds or 1 seconds wall clock time.
---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01
Iteration 1:	Estimated 10193 PSMs with q<0.01
Iteration 2:	Estimated 11236 PSMs with q<0.01
Iteration 3:	Estimated 11461 PSMs with q<0.01
Iteration 4:	Estimated 11509 PSMs with q<0.01
Iteration 5:	Estimated 11560 PSMs with q<0.01
Iteration 6:	Estimated 11576 PSMs with q<0.01
Iteration 7:	Estimated 11602 PSMs with q<0.01
Iteration 8:	Estimated 11617 PSMs with q<0.01
Iteration 9:	Estimated 11617 PSMs with q<0.01
Iteration 10:	Estimated 11616 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
-0.4835	-0.3200	-0.4134	lnrSp
 0.1414	 0.1989	 0.1695	deltLCn
 0.6622	 0.6394	 0.7524	deltCn
 0.6588	 0.6486	 0.6804	Xcorr
-0.0413	 0.0625	-0.0978	Sp
 0.0244	 0.1588	 0.2191	IonFrac
 0.8867	 0.6292	 0.4141	Mass
-0.7489	-0.3031	-0.0249	PepLen
 0.1083	 0.1800	 0.1009	Charge1
 0.0250	 0.0242	 0.0043	Charge2
-0.0471	-0.0610	-0.0250	Charge3
 1.3220	 1.2346	 1.2522	enzN
 1.3377	 1.1510	 1.1172	enzC
-1.9073	-1.7718	-1.6438	enzInt
-0.0159	-0.0088	 0.1201	lnNumSP
 0.0188	 0.0011	 0.0218	dM
 0.0044	 0.0139	 0.0016	absdM
-6.5792	-6.3779	-5.8394	m0
Found 11446 test set PSMs with q<0.01.
Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide.
Selecting pi_0=0.86749
Calculating q values.
New pi_0 estimate on final list yields 7371 target peptides with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 27.73 cpu seconds or 16 seconds wall clock time.
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: percolator-3.05-10.fc38.x86_64
Provides: percolator = 3.05-10.fc38 percolator(x86-64) = 3.05-10.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.25)(64bit) libc.so.6(GLIBC_2.28)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.6)(64bit) libc.so.6(GLIBC_2.7)(64bit) libc.so.6(GLIBC_2.8)(64bit) libc.so.6(GLIBC_2.9)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(GOMP_4.5)(64bit) libgomp.so.1(OMP_1.0)(64bit) libgomp.so.1(OMP_3.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libsqlite3.so.0()(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libstdc++.so.6(CXXABI_1.3.11)(64bit) libstdc++.so.6(CXXABI_1.3.13)(64bit) libstdc++.so.6(CXXABI_1.3.3)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.10)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.5)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libtirpc.so.3()(64bit) libtirpc.so.3(TIRPC_0.3.0)(64bit) libtokyocabinet.so.9()(64bit) libxerces-c-3.2.so()(64bit) libz.so.1()(64bit) libz.so.1(ZLIB_1.2.0)(64bit) rtld(GNU_HASH)
Obsoletes: fido-pi = 0:0
Processing files: percolator-data-3.05-10.fc38.noarch
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.flTAso
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-05
+ DOCDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/doc/percolator-data
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/doc/percolator-data
+ cp -pr ReadMe.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/doc/percolator-data
+ cp -pr src/converters/MSToolkit/RAMP/RAMP-README src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/doc/percolator-data
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.SAGgfh
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-05
+ LICENSEDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/licenses/percolator-data
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/licenses/percolator-data
+ cp -pr license.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/licenses/percolator-data
+ cp -pr RAMP_license_lgpl-2.1.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/licenses/percolator-data
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: percolator-data = 3.05-10.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-static-3.05-10.fc38.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.hsLuck
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-05
+ DOCDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/doc/percolator-static
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/doc/percolator-static
+ cp -pr ReadMe.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/doc/percolator-static
+ cp -pr src/converters/MSToolkit/RAMP/RAMP-README src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/doc/percolator-static
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.jLxFpz
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-05
+ LICENSEDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/licenses/percolator-static
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/licenses/percolator-static
+ cp -pr license.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/licenses/percolator-static
+ cp -pr RAMP_license_lgpl-2.1.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/licenses/percolator-static
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: percolator-static = 3.05-10.fc38 percolator-static(x86-64) = 3.05-10.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-debugsource-3.05-10.fc38.x86_64
Provides: percolator-debugsource = 3.05-10.fc38 percolator-debugsource(x86-64) = 3.05-10.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-debuginfo-3.05-10.fc38.x86_64
Provides: debuginfo(build-id) = 73e72dec98ada9b09f56079c1f0ba06b0ecc0ef8 debuginfo(build-id) = b77f8dc89366b8e7419e06c8e6e54bbfe5f3b3a2 debuginfo(build-id) = daec2c6b8864f07d9e8bc33f735ac76f5cb3b868 debuginfo(build-id) = ebb13a956e750cd71e08b141b398c64f1c921f51 debuginfo(build-id) = f4df8b6481b02fffe3d2213a5ee528964af42f2d debuginfo(build-id) = fec08e9bcedee5e473a0f5504fbe3242457fff5b percolator-debuginfo = 3.05-10.fc38 percolator-debuginfo(x86-64) = 3.05-10.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: percolator-debugsource(x86-64) = 3.05-10.fc38
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64
Wrote: /builddir/build/RPMS/percolator-static-3.05-10.fc38.x86_64.rpm
Wrote: /builddir/build/RPMS/percolator-data-3.05-10.fc38.noarch.rpm
Wrote: /builddir/build/RPMS/percolator-3.05-10.fc38.x86_64.rpm
Wrote: /builddir/build/RPMS/percolator-debugsource-3.05-10.fc38.x86_64.rpm
Wrote: /builddir/build/RPMS/percolator-debuginfo-3.05-10.fc38.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.FYZuIb
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-05
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.65KSuC
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf percolator-rel-3-05 percolator-rel-3-05.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild percolator-3.05-10.fc38.src.rpm
Finish: build phase for percolator-3.05-10.fc38.src.rpm
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-x86_64-1668321698.617486/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-x86_64-1668321698.617486/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-x86_64-1668321698.617486/root/var/log/dnf.log
INFO: Done(/var/lib/copr-rpmbuild/results/percolator-3.05-10.fc38.src.rpm) Config(child) 7 minutes 2 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
Finish: run
Running RPMResults tool